Identification of protective antigenic determinants of porcine reproductive and respiratory syndrome virus and uses thereof

ABSTRACT

The invention relates to a polypeptide of a protective antigenic determinant (PAD polypeptide) of porcine reproductive and respiratory syndrome virus (PRRSV) and nucleic acids encoding a PAD polypeptide. The PAD polypeptide and nucleic acids encoding a PAD polypeptide are useful in the development of antibodies directed to PAD, vaccines effective in providing protection against PRRSV infection, and diagnostic assays detecting the presence of PAD antibodies generated by a PAD-specific vaccine. The invention also discloses methods of generating antibodies to PAD, for vaccinating a pig to provide protection from PRRSV infections, a method of preparing the vaccine, a method of treating PRRSV infections in a pig, and a method of detecting antibodies to PAD of PRRSV.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is a Divisional of U.S. application Ser. No. 13/533,167 filed Jun.26, 2012, which is a Divisional of U.S. application Ser. No. 12/782,030filed May 18, 2010, which is a Continuation of U.S. Ser. No. 12/345,259filed Dec. 29, 2008, now U.S. Pat. No. 7,763,428 issued on Jul. 27,2010, which is a Divisional of U.S. application Ser. No. 11/564,717filed Nov. 29, 2006, now U.S. Pat. No. 7,622,254, issued on Nov. 24,2009, which claims priority under 35 U.S.C. §119 of ProvisionalApplication Ser. No. 60/740,519 filed Nov. 29, 2005, and whichapplications are hereby incorporated by reference in their entirety.

GRANT REFERENCE

This invention was made with government support under Grant No.2004-35605-14197 awarded by USDA/CREES. The United States government hascertain rights in the invention.

FIELD OF THE INVENTION

Embodiments of the invention relate generally to the field of porcinereproductive and respiratory syndrome virus (PRRSV) and moreparticularly to the discovery of a novel protective antigenicdeterminant (PAD) of PRRSV and its use in vaccines, treatments, anddiagnostic assays.

BACKGROUND OF THE INVENTION

In 1987, the swine-producing industry in the United States experiencedan unknown infectious disease which had a serious economic impact on theswine industry. The disease syndrome was reported in Europe includingGermany, Belgium, the Netherlands, Spain and England.

The disease is characterized by reproductive failure, respiratorydisease and various clinical signs including loss of appetite, fever,dyspnea, and mild neurologic signs. A major component of the syndrome isreproductive failure which manifests itself as premature births, lateterm abortions, pigs born weak, stillbirths, mummified fetuses,decreased farrowing rates, and delayed return of estrus. Clinical signsof respiratory disease are most pronounced in pigs under 3-weeks-of-agebut are reported to occur in pigs at all stages of production. Affectedpiglets grow slowly, have roughened hair coats, respiratory distress(“thumping”), and increased mortality.

The disease syndrome has been referred to by many different termsincluding mystery swine disease (MSD), porcine epidemic abortion andrespiratory syndrome (PEARS), swine infertility and respiratory syndrome(SIRS). The name now commonly used is porcine reproductive andrespiratory syndrome (PRRS); this term will be employed throughout thispatent application.

PRRSV preferentially grows in alveolar lung macrophages (Wensvoort etal., 1991). A few cell lines, such as CL2621 and other cell lines clonedfrom the monkey kidney cell line MA-104 are also susceptible to thevirus. Some well known PRRSV strains are known under accession numbersCNCM I-1102, I-1140, I-1387, I-1388, ECACC V93070108, or ATCC VR 2332,VR 2385, VR 2386, VR 2429, VR 2474, and VR 2402. The genome of PRRSV is15 kb in length and contains genes encoding the RNA dependent RNApolymerase (ORF1a and ORF1b) and genes encoding structural proteins(ORFs 2 to 7; Meulenberg et al., 1993 and Meulenberg et al., 1996). ORF5encodes the major envelope glycoprotein, designated GP5. The ORFs 2, 3,and 4 encode glycoproteins designated GP2, GP3, and GP4, respectively.These glycoproteins are less abundantly present in purified virions ofthe Lelystad virus isolate of PRRSV. The GP5 protein is approximately200 amino acids in length and is 25 kDa in molecular weight and forms adi-sulfide-linked heterodimer with the matrix protein M encoded by ORF6in the ER. The M protein is approximately 190 amino acids in length, is19 kDa and is non-glycosylated. The nucleocapsid protein N is encoded byORF7. The analysis of the genome sequence of PRRSV isolates from Europeand North America, and their reactivity with monoclonal antibodies hasproven that they represent two different antigenic types. The isolatesfrom these continents are genetically distinct and must have divergedfrom a common ancestor relatively long ago (Murtaugh et al., 1995).

The genomic organization of arteriviruses resembles coronaviruses andtoroviruses in that their replication involves the formation of a3′-coterminal nested set of subgenomic mRNAs (sg mRNAs) (Chen et al.,1993, J. Gen. Virol. 74:643-660; Den Boon et al., 1990, J. Virol.,65:2910-2920; De Vries et al., 1990, Nucleic Acids Res., 18:3241-3247;Kuo et al., 1991, J. Virol., 65:5118-5123; Kuo et al., 1992; U.S.application Ser. Nos. 08/131,625 and 08/301,435). Partial sequences ofseveral North American isolates have also been determined (U.S.application Ser. Nos. 08/131,625 and 08/301,435; Mardassi et al., 1994,J. Gen. Virol., 75:681-685). Currently available vaccines either do notinduce viral neutralizing VN antibodies or induce them at inadequatelevels needed for protection against PRRSV infection. There arecurrently no commercially available products containing antibodies forthe prevention of PRRSV infection or treatment of PRRS. Currentlyavailable commercial vaccines do not provide adequate protection againstPRRS. Conservative estimates indicate that PRRS is costing the USindustry $600 million per year.

For these and other reasons, there is a need for the present invention.

BRIEF SUMMARY OF THE INVENTION

The present inventors are the first to recognize a protective antigenicdeterminant (PAD) for porcine reproductive and respiratory syndromevirus (PRRSV) that provides treatment for and protection against PRRSVinfection. Surprisingly, the present inventors have identified thatglycoprotein 5 (GP5), matrix (M) protein, or a heterodimer of the GP5and M protein of PRRSV linked by a disulfide bond gives rise to a PADthat provides protection against PRRSV infections. The disulfide bondconnecting the M protein with the GP5 protein results from a cysteineamino acid of the M protein at position 9 in North American and atposition 8 EU PRRSV strains and a cysteine amino acid of the GP5 proteinlocated at position 48 of North American PRRSV strains and position 50of European PRRSV strains.

In one embodiment, the invention provides one or more isolatedpolypeptides comprising an antigenic sequence comprising glycoprotein 5(GP5) of porcine reproductive and respiratory syndrome virus (PRRSV),wherein the GP5 protein has varying N-glycosylation patterns ofasparagine amino acids located at positions 1-44 of the GP5 protein inNorth American PRRSV strains or at positions 1-46 of the GP5 protein inEuropean PRRSV strains. In yet another embodiment, the inventionprovides an isolated polypeptide comprising an antigenic sequencecomprising matrix (M) protein of porcine reproductive and respiratorysyndrome virus (PRRSV). In another embodiment, the antigenic sequenceincludes the GP5 sequence as described above and a matrix protein (Mprotein) of PRRSV, wherein the GP5 protein is linked to said M proteinby a disulfide bond, resulting from a cysteine amino acid of the Mprotein at position 9 in North American and at position 8 in EU PRRSVstrains and a cysteine amino acid located at position 48 of the GP5protein in North American PRRSV strains or from a cysteine amino acidlocated at position 50 in European PRRSV strains so that a GP5-Mheterodimer is produced. In one aspect of the invention, the PADincludes a GP5-M heterodimer comprising the ectodomain of GP5 and theectodomain of M.

In yet another embodiment, the invention provides an isolated nucleicacid encoding any of the PAD polypeptides of the present invention.Consequently, the invention provides for methods for generatingantibodies against one or more protective antigenic determinant (PAD) ofPRRSV, for preparing a vaccine against at least one PAD of PRRSV, ofvaccinating pigs, for preventing or treating a PRRSV infection in a pig,and for detecting antibodies against at least one protective antigenicdeterminant (PAD) of PRRSV in an animal.

The present inventors contemplate a method for generating antibodiesagainst at least one protective antigenic determinant (PAD) of PRRSVcomprising providing at least one PAD polypeptide or nucleic acidencoding a PAD polypeptide and administering the peptide or nucleic acidto an animal subject. Also disclosed herein is a method for generatingantibodies against at least one protective antigenic determinant (PAD)of PRRSV comprising: providing a PAD polypeptide or a nucleic acidencoding a PAD polypeptide and administering the peptide or nucleic acidto an animal subject. The invention also provides a method for preparinga vaccine against at least one PAD of PRRSV including a PAD polypeptideor a nucleic acid encoding a PAD polypeptide. In another embodiment, amethod of vaccinating pigs includes administering to a pig, the vaccinethat includes at least one PAD polypeptide or a nucleic acid encoding aPAD polypeptide in an amount effective for protecting against PRRSVinfection when administered to a susceptible pig. The present inventorscontemplate a method for preventing or treating a PRRSV infection in apig comprising administering to a pig a therapeutically effective amountof a vaccine that has at least one PAD polypeptide or a nucleic acidencoding at least one PAD polypeptide. Yet another method for treatingPRRSV infections in a pig comprises administering an antibody against atleast one protective antigenic determinant (PAD) of PRRSV to an animalin need of treatment. Also contemplated is a method for detectingantibodies against at least one protective antigenic determinant (PAD)of PRRSV in an animal. This method includes incubating a biologicalsample, including antiserum, from an animal, for example, a pig, with aPAD polypeptide for a time sufficient for antibody binding to takeplace, and determining the binding of the antibody to the polypeptide.

In another embodiment, the invention provides an isolated antibodydirected against at least one PAD polypeptide or a nucleic acid encodinga PAD polypeptide. The invention also discloses a vaccine for protectingagainst PRRSV infection comprising administering at least one PADpolypeptide or a nucleic acid encoding at least one PAD polypeptide inan amount effective for protecting against PRRSV infection. In anotheraspect, the vaccine also includes a physiologically acceptable carrier.In yet another embodiment, the invention provides for a kit thatcomprises at least one of the following: a PAD polypeptide, a nucleicacid encoding a PAD polypeptide, an antibody directed against a PADpolypeptide, or a vaccine including a PAD polypeptide or a nucleic acidencoding a PAD polypeptide.

Accordingly, an object of the present invention is to provide anisolated polypeptide comprising a PAD of PRRSV that includes the GP5 ofPRRSV.

An object of the present invention is to provide an isolated polypeptidecomprising a PAD of PRRSV that includes the matrix protein (M) of PRRSV.

A further still object of the present invention is to provide anisolated polypeptide comprising a PAD of PRRSV that includes the GP5 ofPRRSV linked by a disulfide bond to the M protein of PRRSV.

Yet another object of the present invention is to provide an isolatednucleic acid encoding a PAD polypeptide.

Still another object of the present invention is to provide a method forgenerating antibodies against a protective antigenic determinant (PAD)of PRRSV. A further object of the present invention is to provide amethod for preparing a vaccine.

Another object of the present invention to provide a method ofvaccinating pigs against PAD of PRRSV effective for protecting pigsagainst PRRSV infections.

It is an object of the present invention to provide a vaccine againstPAD of PRRSV capable of protecting pigs against PRRSV infections.

It is a further object of the present invention to provide a method oftreating or preventing a PRRSV infection in a pig.

Still another object of the present invention is to provide a method fordetecting antibodies against a protective antigenic determinant (PAD) ofPRRSV in an animal.

It is a further object of the present invention to provide an antibodythat immunologically binds to a PAD polypeptide of PRRSV.

Yet another object of the present invention to provide a vaccineeffective for protecting against PRRSV infection.

It is a further object of the present invention to provide a diagnostickit for assaying or detecting antibodies to PAD of PRRSV.

These and other embodiments of the invention will become apparent uponreference to the following Detailed Description. All referencesdisclosed herein are hereby incorporated by reference in theirentireties as if each was incorporated individually.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Amino acid comparison of PRRSV GP5 signal sequence andectodomain (amino acids 1-60). The neutralizing epitope of GP5 isunderlined. N-glycosylation sites are in bold. Presence or location ofN-glycans in the ectodomain may be related to susceptibility to ordevelopment of PRRSV neutralizing antibodies.

FIG. 2: Nonreduced Western immunoblot comparing VR2332 and HLV013antisera. Pigs were immunized with either VR2332 or HLV013 on Day 1. Allpigs were challenged with VR2332 on Day 90. Protein concentration wasthe same for both antigens tested. Antisera was diluted 1:4000. Lane 1is standard ladder. Lane 2 is IA97-7895 antigen and normal swine serum.Lane 3 is HLV013 antigen and normal swine serum. Lane 4 is IA97-7895antigen and HLV013 antisera 42 days post-inoculation (p.i.). Lane 5 isHLV013 antigen and HLV013 antisera 42 days p.i. Lane 6 is IA97-7895antigen and VR2332 antisera 42 days p.i. Lane 7 is HLV013 antigen andVR2332 antisera 42 days p.i. Lane 8 is IA97-7895 antigen and HLV013antisera 104 days p.i. Lane 9 is HLV013 antigen and HLV013 antisera 104days p.i. Lane 10 is IA97-7895 antigen and VR2332 antisera 104 days p.i.Lane 11 is HLV013 antigen and VR2332 antisera 104 days p.i. Lane 12 isstandard ladder.

FIG. 3: Non-reduced western blot of different serum samples from pigafter live PRRSV inoculation. As the neutralizing antibody (FFN) titersincrease, so does the intensity of antibody reaction to the GP-Mheterodimer indicating the protective role of GP-M specific antibodies.The intensity of the antibody reaction to GP5 monomer however decreases.A very slight increase in reaction density can also be seen for N-Nhomodimer and Matrix monomer however previous studies have shown thatantibodies specific for these proteins are not protective. Lane1—ladder, Lane 2—neut titer=256, Lane 3—neut titer=1024, Lane 4—neuttiter=2048.

FIG. 4: Neutralizing antibody response in pigs given either 2inoculations of HLV013 or VR2332. Geometric mean titers of 6 pigs pergroup. *Group 1 pigs (control) remained negative for neutralizingantibodies throughout the study. Compared to Group 2 pigs, Group 3 pigshad a quicker, more robust onset of neutralizing antibodies tohomologous and heterologous virus.

FIG. 5: Neutralizing antibody responses after inoculation with aheterologous strain (MN184). Please refer to Example 2 for a descriptionof the individual lanes. This trial provides evidence that there is alarge difference between the protective antibody responses to strainsthat differ in glycosylation. HLV013 lacking glycans prior to aa44 had afaster, more robust antibody response pre-challenge with morecross-reactivity when compared to VR2332. Post-challenge pigs inoculatedwith HLV013 had a faster anamnestic response and a faster response timein generating antibodies to the challenge strain. Note that the GP5-Mheterodimer of MN184 and VR2332 are slightly higher (kDa) due topresence of additional N-glycans

FIG. 6: Comparison of geometric mean neutralizing antibody titersgenerated in example 3 against different PRRSV glycantype groups.

FIG. 7: Non-reduced western blot comparing the antibody reactivity ofpigs from Groups 1 and 2. See table in example 3 for description of lanecontents. This figure shows that the increase in protective antibodiesgenerated in the HLV013-HLV093 scheme compared to HLV013 alone is due toan increased reactivity to the GP5-M heterodimer.

FIG. 8: Non-reduced western blot comparing antibody profiles ofHLV013-HLV093 inoculated pig (Lane 1) to a VR2332-VR2332 inoculated pig(Lane 3). A ladder is shown in Lane 2. Purified VR2332 protein was usedas the test antigen (10 ug per lane). Primary antibody dilution was1:100 and secondary was 1:2000. The anti-VR2332 FFN titer in Lane 1 was256 and in Lane 3 was 16. Thus the HVL013-HLV093 inoculated pigsdeveloped a higher anti-VR2332 neutralizing titer than pigs inoculatedwith VR2332-VR2332 itself. A clear difference in reaction to the GP-Mheterodimer is also seen on the western blot.

FIG. 9: VR2332 GP5-M Heterodimer. Dashed lines indicate N-linked glycans(not to scale).

FIG. 10: HLV013 GP5-M Heterodimer.

FIG. 11: HLV093 GP5-M Heterodimer.

FIG. 12: HLV092 GP5-M Heterodimer.

FIG. 13: Lelystad GP5-M Heterodimer.

FIG. 14: Peptide ELISA data. The peptide ELISA detects antibody to thevirus neutralizing epitope of PRRSV GP5. Pigs (n=6 per group) wereinoculated with equal titers of either HLV013 or VR2332 PRRSV on Day 0.

FIG. 15: Average IDEXX ELISA response in pigs inoculated with eitherHLV013 crude viral antigen (CVA) or Intervet's killed vaccine.

FIG. 16. Neutralizing epitope with no glycan block or shield.

FIG. 17. Neutralizing epitope with glycan block (BNE).

FIG. 18. Neutralizing epitope with glycan shield only.

FIG. 19. Highly glycoyslated strain with glycan block and glycan shield.

FIG. 20. HLV013 complete ORF 5 and 6, corresponding to GP5 and M proteinrespectively.

FIGS. 21A and 21B. ORF6 sequences that encode the matrix protein.

FIGS. 22A and 22B. Examples of amino acid sequences of PRRSV GP5 signalsequence and ectodomain (SEQ ID NOS:44-87 et. seq.).

FIG. 23. HLV092 complete ORF 5 corresponding to GP5.

FIG. 24. HLV093 complete ORF 5 corresponding to GP5.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

The present inventors are first to identify a protective antigenicdeterminant (PAD) for porcine reproductive and respiratory syndromevirus (PRRSV) that provides treatment for and protection against PRRSVinfection.

It is known that there is reduced or no heterologous protection withPRRSV vaccines. The present inventors propose that changes in theN-glycosylation patterns of asparagines in the glycoprotein 5 (GP5)ectodomain of PRRSV or changes in the conformation of GP5 frominteractions with another protein, for example, the M protein of PRRSV,play an important role in providing protection against PRRSV. In oneaspect, the GP5's structure is altered by forming a heterodimer with theM protein of PRRSV. See FIGS. 9-12. These changes in nucleotide or aminoacid sequences may result in a conformational change or the addition orsubtraction of N-linked glycosylation sites on the GP5 ectodomain. Thepresent inventors also contemplate that changes to the M protein ofPRRSV may also affect the heterodimer conformation. The presentinventors believe that changes in the N-glycosylation patterns ofasparagines in the glycoprotein 5 (GP5) ectodomain of PRRSV or a GP5-Mheterodimer of glycoprotein 5 (GP5) and a matrix protein (M protein) ofPRRSV linked by a disulfide bond gives rise to a PAD that providesprotection against PRRSV infections. The disulfide bond connecting the Mprotein with the GP5 protein results from a cysteine amino acid locatedon the GP5 protein at position 48 for North American strains and atposition 50 for European strains. In one aspect, the cysteine is locatedat position 9 of the M protein in North American PRRSV strains and atposition 8 in European PRRSV strains.

In one embodiment, the invention provides one or more PADs that includesisolated polypeptides comprising an antigenic sequence comprisingglycoprotein 5 (GP5) of PRRSV, wherein the GP5 protein has varyingN-glycosylation patterns of asparagine amino acids located at positions1-44 of the GP5 protein in North American PRRSV strains or at positions1-46 of the GP5 protein in European PRRSV strains. In one aspect, thePAD includes the ectodomain of GP5. In another aspect, the PAD includesthe neutralizing epitope of the ectodomain of GP5. In one aspect, theneutralizing epitope has an amino acid sequence of SHLQLIYNL (SEQ IDNO:92).

In yet another embodiment, the invention provides a PAD that includes anisolated polypeptide comprising an antigenic sequence comprising matrix(M) protein of PRRSV. In one aspect, the antigenic sequence is theectodomain of the M protein. In one aspect, the ectodomain includes thefirst 30 amino acids or less of the M protein of NA or EU PRRSV strains.

In another embodiment, the antigenic sequence includes the GP5 sequenceas described herein and a matrix protein (M protein) of PRRSV asdescribed herein, wherein the GP5 protein is linked to the M protein bya disulfide bond, resulting from a cysteine amino acid of the M proteinat position 9 in North American and at position 8 in EU PRRSV strainsand a cysteine amino acid located at position 48 of the GP5 protein inNorth American PRRSV strains or from a cysteine amino acid located atposition 50 in European PRRSV strains so that a GP5-M heterodimer isproduced.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-35 in the NA PRRSV GP5 protein. In another aspect, aPAD of GP5 may have a glycan at position 44 in the NA PRRSV GP5 protein.In another aspect, a PAD of GP5 may have a glycan at position 44 in theNA PRRSV GP5 and have glycans present or absent in amino acids 1-35 inthe NA PRRSV GP5 protein, for example, as found in some NA PRRSVstrains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-35 in the NA PRRSV GP5 protein. In anotheraspect, a PAD of GP5-M heterodimer may have a glycan at position 44 inthe NA PRRSV GP5 protein. In another aspect, a PAD of GP5-M heterodimermay have a glycan at position 44 in the NA PRRSV GP5 and have glycanspresent or absent in amino acids 1-35 in the NA PRRSV GP5 protein, forexample, as found in some NA PRRSV strains.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-37 in the EU PRRSV GP5 protein, as found in Lelystad.In another aspect, a PAD of GP5 may have a glycan at position 46 in theEU PRRSV GP5 protein. In another aspect, a PAD of GP5 may have a glycanat position 46 in the EU PRRSV GP5 and have glycans present or absent inamino acids 1-37 in the EU PRRSV GP5 protein, for example, as found insome EU PRRSV strains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-37 in the EU PRRSV GP5 protein, as foundin Lelystad. In another aspect, a PAD of GP5-M heterodimer may have aglycan at position 46 in the EU PRRSV GP5 protein. In another aspect, aPAD of GP5-M heterodimer may have a glycan at position 46 in the EUPRRSV GP5 and have glycans present or absent in amino acids 1-37 in theEU PRRSV GP5 protein, for example, as found in some EU PRRSV strains.

In another embodiment, the PAD includes an antigenic sequence comprisingamino acids 36-45 of GP5 of NA PRRSV and the ectodomain of the M proteinof PRRSV. In another aspect, the M protein ectodomain includes aminoacids 1-30. In another embodiment of the invention the PAD includes anantigenic sequence comprising amino acids 38-47 of GP5 of EU PRRSV andthe ectodomain of the M protein of PRRSV. The GP5 protein may havevarying N-glycosylation patterns of asparagine amino acids located atpositions 1-44 of the GP5 protein in North American PRRSV strains or atpositions 1-46 of the GP5 protein in European PRRSV strains. Thesevariations are also included in PADs of the invention.

Thus, with the identification of a PAD comprising a GP5 protein that isN-glycosylated or non-N-glycosylated from amino acids 1-46 of the GP5ectodomain or an M protein or a GP5-M heterodimer of a M proteindisulfide linked to a GP5 protein that is N-glycosylated ornon-N-glycosylated from amino acids 1-46 of the GP5 ectodomain of PRRSV,it is possible to develop an effective vaccine against PRRSV.

A vaccine according to the present invention may include a PADpolypeptide as described herein, and may include but is not limitedimmunogenic fragments, derivatives, homologues or variants thereof,comprising an amino acid sequence at least 65% identical, 80% identical,95% identical or 100% identical to any one of the PAD amino acidsequences of FIG. 1. SEQ ID NOS: 1-11.

The PADs according to the invention will include derivatives, homologuesor variants thereof of, which fragments can be readily screened forimmunogenic activity, as well as immunogenic fragments, for example, ofthose shown in FIGS. 1 and 21 (SEQ ID NOS: 1-11 and 29-43). Thus,derivatives, homologues or variants thereof can be tested usingneutralizing assays or tested for the derivatives, homologues orvariants thereof ability to provide protection against pigs challengedwith a heterologous PRRSV using assays such as the fluorescent focusingneutralizing (FFN) test or Western blot assay for the heterodimer may beused to give an indication of heterologous antibody production. Thus,specific fragments may include but are not limited to fragments havingamino acid sequences shown in FIGS. 1 and 21 (SEQ ID NO: 1-11 and29-43). It is logical to presume that fragments of GP5-M heterodimersmay provide similar degrees of protection.

In one aspect, the vaccine may be attenuated, inactivated, subunit,recombinant, vector, or DNA based. In still a further aspect, thevaccines may be used in an immunization scheme or protocol. In anotheraspect of the invention, a PAD may be utilized to produce antibodies todiagnose whether a PSSRV vaccination based on a PAD was successful or toproduce vaccines for prophylaxis and/or treatment of PRRSV infections.In addition to use as vaccines, PAD polypeptides of the presentinvention can be used as antigens to stimulate the production ofantibodies for use in passive immunotherapy, for use as diagnosticreagents, and for use as reagents in other processes such as affinitychromatography.

DEFINITIONS

As used herein, a “porcine reproductive and respiratory syndrome virus”or “PRRSV” refers to a virus which causes the diseases PRRS, PEARS,SIRS, MSD and/or PIP (the term “PIP” now appears to be disfavored),including the Iowa strain of PRRSV, other strains of PRRSV found in theUnited States (e.g., VR 2332), strains of PRRSV found in Canada (e.g.,IAF-exp91), strains of PRRSV found in Europe (e.g., Lelystad virus,PRRSV-10), and closely-related variants of these viruses which may haveappeared and which will appear in the future.

An unaffected pig is a pig which has either not been exposed to aporcine reproductive and respiratory disease infectious agent, or whichhas been exposed to a porcine reproductive and respiratory diseaseinfectious agent such as PRRSV but is not showing symptoms of thedisease. An affected pig is one which shows symptoms of PRRS or fromwhich PRRSV can be isolated.

The terms “treating” or “treatment”, as used herein, refer to reductionor alleviation of at least one adverse effect or symptom of PRRSVinfection. The clinical signs or symptoms of PRRS may include weightloss, decreased weight gain, lethargy, respiratory distress, “thumping”(forced expiration), fevers, roughened haircoats, sneezing, coughing,eye edema and occasionally conjunctivitis. Lesions may include grossand/or microscopic lung lesions, myocarditis, lymphadenitis,encephalitis and rhinitis. In addition, less virulent and non-virulentforms of PRRSV and of the Iowa strain have been found, which may causeeither a subset of the above symptoms or no symptoms at all. Lessvirulent and non-virulent forms of PRRSV can be used according to thepresent invention to provide protection against porcine reproductive andrespiratory diseases nonetheless.

As used herein, an “ORF” refers to an open reading frame, orpolypeptide-encoding segment, isolated from a viral genome, including aPRRSV genome. In the present polynucleic acid, an ORF can be included inpart (as a fragment) or in whole, and can overlap with the 5′- or3′-sequence of an adjacent ORF.

“Nucleic acid” or “polynucleotide” as used herein refers to purine- andpyrimidine-containing polymers of any length, either polyribonucleotidesor polydeoxyribonucleotide or mixed polyribo-polydeoxyribonucleotides.This includes single- and double-stranded molecules, i.e., cDNA, mRNA,DNA-DNA, DNA-RNA and RNA-RNA hybrids, as well as “protein nucleic acids”(PNA) formed by conjugating bases to an amino acid backbone. This alsoincludes nucleic acids containing modified bases.

A “vector” is any means for the transfer of a nucleic acid into a hostcell. A vector may be a replicon to which another DNA segment may beattached so as to bring about the replication of the attached segment. A“replicon” is any genetic element (e.g., plasmid, phage, cosmid,chromosome, virus) that functions as an autonomous unit of DNAreplication in vivo, i.e., capable of replication under its own control.The term “vector” includes both viral and nonviral means for introducingthe nucleic acid into a cell in vitro, ex vivo or in vivo. Viral vectorsinclude alphavirus, retrovirus, adeno-associated virus, pox,baculovirus, vaccinia, herpes simplex, Epstein-Barr and adenovirusvectors. Non-viral vectors include, but are not limited to plasmids,liposomes, electrically charged lipids (cytofectins), DNA-proteincomplexes, and biopolymers. In addition to a nucleic acid, a vector mayalso contain one or more regulatory regions, and/or selectable markersuseful in selecting, measuring, and monitoring nucleic acid transferresults (transfer to which tissues, duration of expression, etc.).

A “cassette” refers to a segment of DNA that can be inserted into avector at specific restriction sites. The segment of DNA encodes apolypeptide of interest, and the cassette and restriction sites aredesigned to ensure insertion of the cassette in the proper reading framefor transcription and translation.

A cell has been “transfected” by exogenous or heterologous DNA when suchDNA has been introduced inside the cell.

A cell has been “transformed” by exogenous or heterologous DNA when thetransfected DNA effects a phenotypic change. The transforming DNA can beintegrated (covalently linked) into chromosomal DNA making up the genomeof the cell.

A “nucleic acid molecule” refers to the phosphate ester polymeric formof ribonucleosides (adenosine, guanosine, uridine or cytidine; “RNAmolecules”) or deoxyribonucleosides (deoxyadenosine, deoxyguanosine,deoxythymidine, or deoxycytidine; “DNA molecules”), or any phosphoesteranalogs thereof, such as phosphorothioates and thioesters, in eithersingle stranded form, or a double-stranded helix. Double strandedDNA-DNA, DNA-RNA and RNA-RNA helices are possible. The term nucleic acidmolecule, and in particular DNA or RNA molecule, refers only to theprimary and secondary structure of the molecule, and does not limit itto any particular tertiary forms. Thus, this term includesdouble-stranded DNA found, inter alia, in linear or circular DNAmolecules (e.g., restriction fragments), plasmids, and chromosomes. Indiscussing the structure of particular double-stranded DNA molecules,sequences may be described herein according to the normal convention ofgiving only the sequence in the 5′ to 3′ direction along thenontranscribed strand of DNA (i.e., the strand having a sequencehomologous to the mRNA). A “recombinant DNA molecule” is a DNA moleculethat has undergone a molecular biological manipulation.

As used herein, a “polypeptide” refers generally to peptides andproteins having more than eight amino acids.

“Conservatively modified variants” applies to both amino acid andnucleic acid sequences. With respect to particular nucleic acidsequences, conservatively modified variants refers to those nucleicacids which encode identical or essentially identical amino acidsequences, or where the nucleic acid does not encode an amino acidsequence, to essentially identical sequences. Because of the degeneracyof the genetic code, a large number of functionally identical nucleicacids encode any given polypeptide. For instance, the codons CGU, CGC,CGA, CGG, AGA, and AGG all encode the amino acid arginine. Thus, atevery position where an arginine is specified by a codon, the codon canbe altered to any of the corresponding codons described without alteringthe encoded polypeptide. Such nucleic acid variations are “silentsubstitutions” or “silent variations,” which are one species of“conservatively modified variations.” Every polynucleotide sequencedescribed herein which encodes a polypeptide also describes everypossible silent variation, except where otherwise noted. Thus, silentsubstitutions are an implied feature of every nucleic acid sequencewhich encodes an amino acid. One of skill will recognize that each codonin a nucleic acid (except AUG, which is ordinarily the only codon formethionine) can be modified to yield a functionally identical moleculeby standard techniques. In some embodiments, the nucleotide sequencesthat encode a PAD are preferably optimized for expression in aparticular host cell (e.g., yeast, mammalian, plant, fungal, and thelike) used to produce the enzymes.

As to amino acid sequences, one of skill will recognize that individualsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alters, adds or deletes a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” referred to herein as a “variant”where the alteration results in the substitution of an amino acid with achemically similar amino acid. Conservative substitution tablesproviding functionally similar amino acids are well known in the art.See, for example, Davis et al., “Basic Methods in Molecular Biology”Appleton & Lange, Norwalk, Conn. (1994). Such conservatively modifiedvariants are in addition to and do not exclude polymorphic variants,interspecies homologs, and alleles of the invention.

The following eight groups each contain amino acids that areconservative substitutions for one another: 1) Alanine (A), Glycine (G);2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine(Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L),Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y),Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C),Methionine (M) (see, e.g., Creighton, 1984, Proteins).

The terms “identical” or percent “identity,” in the context of two ormore nucleic acids or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same(i.e., about 70% identity, preferably 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identityover a specified region (e.g., the sequence of the neutralizing epitopeof a GP5 protein of PRRSV), when compared and aligned for maximumcorrespondence over a comparison window or designated region) asmeasured using a BLAST or BLAST 2.0 sequence comparison algorithms withdefault parameters described below, or by manual alignment and visualinspection. Such sequences are then said to be “substantiallyidentical.” This definition also refers to the compliment of a testsequence. The definition also includes sequences that have deletionsand/or additions, as well as those that have substitutions. As describedbelow, the preferred algorithms can account for gaps and the like.Preferably, the identity exists over a region that is at least about 25amino acids or nucleotides in length, or more preferably over a regionthat is 50-100 amino acids or nucleotides in length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters can be used, or alternative parameters can be designated. Thesequence comparison algorithm then calculates the percent sequenceidentities for the test sequences relative to the reference sequence,based on the program parameters.

A “comparison window”, as used herein, includes reference to a segmentof any one of the number of contiguous positions selected from the groupconsisting of from 20 to 600, usually about 50 to about 200, moreusually about 100 to about 150 in which a sequence can be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned. Methods of alignment of sequencesfor comparison are well-known in the art. Optimal alignment of sequencesfor comparison can be conducted, e.g., by the local homology algorithmof Smith & Waterman, 1991, Adv. Appi. Math. 2:482, by the homologyalignment algorithm of Needleman & Wunsch, 1970, J. Mol. Biol. 48:443,by the search for similarity method of Pearson & Lipman, 1988, Proc.Nat'l. Acad. Sci. USA 85:2444, by computerized implementations of thesealgorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin GeneticsSoftware Package, Genetics Computer Group, 575 Science Dr., Madison,Wis.), or by manual alignment and visual inspection (see, e.g., CurrentProtocols in Molecular Biology (Ausubel et al., eds. 1995 supplement).

Another example of algorithm that is suitable for determining percentsequence identity and sequence similarity are the BLAST and BLAST 2.0algorithms, which are described in Altschul et al., 1977, Nuc. AcidsRes. 25:3389-3402 and Altschul et al., 1990, J. Mol. Biol. 215:403-410,respectively. Software for performing BLAST analyses is publiclyavailable through the National Center for Biotechnology Information(http://world wide web at ncbi.nlm.nih.gov/). This algorithm involvesfirst identifying high scoring sequence pairs (HSPs) by identifyingshort words of length W in the query sequence, which either match orsatisfy some positive-valued threshold score T when aligned with a wordof the same length in a database sequence. T is referred to as theneighborhood word score threshold (Altschul et al., supra). Theseinitial neighborhood word hits act as seeds for initiating searches tofind longer HSPs containing them. The word hits are extended in bothdirections along each sequence for as far as the cumulative alignmentscore can be increased. Cumulative scores are calculated using, fornucleotide sequences, the parameters M (reward score for a pair ofmatching residues; always >0) and N (penalty score for mismatchingresidues; always <0). For amino acid sequences, a scoring matrix is usedto calculate the cumulative score. Extension of the word hits in eachdirection are halted when: the cumulative alignment score falls off bythe quantity X from its maximum achieved value; the cumulative scoregoes to zero or below, due to the accumulation of one or morenegative-scoring residue alignments; or the end of either sequence isreached. The BLAST algorithm parameters W, T, and X determine thesensitivity and speed of the alignment. The BLASTN program (fornucleotide sequences) uses as defaults a wordlength (W) of 11, anexpectation (E) or 10, M=5, N=−4 and a comparison of both strands. Foramino acid sequences, the BLASTP program uses as defaults a wordlengthof 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (seeHenikoff & Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915)alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparisonof both strands.

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin & Altschul, 1993,Proc. Nat'l. Acad. Sci. USA 90:5873-5787). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide or amino acid sequences would occur by chance. Forexample, a nucleic acid is considered similar to a reference sequence ifthe smallest sum probability in a comparison of the test nucleic acid tothe reference nucleic acid is less than about 0.2, more preferably lessthan about 0.01, and most preferably less than about 0.001.

An indication that two nucleic acid sequences or polypeptides aresubstantially identical is that the polypeptide encoded by the firstnucleic acid is immunologically cross reactive with the antibodiesraised against the polypeptide encoded by the second nucleic acid, asdescribed below. Thus, a polypeptide is typically substantiallyidentical to a second polypeptide, for example, where the two peptidesdiffer only by conservative substitutions. Another indication that twonucleic acid sequences are substantially identical is that the twomolecules or their complements hybridize to each other under stringentconditions, as described below. Yet another indication that two nucleicacid sequences are substantially identical is that the same primers canbe used to amplify the sequence.

As used herein, a protein or peptide is said to be “isolated” or“purified” when it is substantially free of cellular material or free ofchemical precursors or other chemicals. The variant peptides of thepresent invention can be purified to homogeneity or other degrees ofpurity. The level of purification will be based on the intended use. Thecritical feature is that the preparation allows for the desired functionof the variant peptide, even if in the presence of considerable amountsof other components.

In some uses, “substantially free of cellular material” includespreparations of the variant peptide having less than about 30% (by dryweight) other proteins (i.e., contaminating protein), less than about20% other proteins, less than about 10% other proteins, or less thanabout 5% other proteins. When the variant peptide is recombinantlyproduced, it can also be substantially free of culture medium, i.e.,culture medium represents less than about 20% of the volume of theprotein preparation.

The language “substantially free of chemical precursors or otherchemicals” includes preparations of the variant peptide in which it isseparated from chemical precursors or other chemicals that are involvedin its synthesis. In one embodiment, the language “substantially free ofchemical precursors or other chemicals” includes preparations of thevariant protein having less than about 30% (by dry weight) chemicalprecursors or other chemicals, less than about 20% chemical precursorsor other chemicals, less than about 10% chemical precursors or otherchemicals, or less than about 5% chemical precursors or other chemicals.

The isolated variant proteins can be purified from cells that naturallyexpress it, purified from cells that have been altered to express it(recombinant), or synthesized using known protein synthesis methods. Forexample, a nucleic acid molecule encoding the variant PAD protein iscloned into an expression vector, the expression vector introduced intoa host cell and the variant protein expressed in the host cell. Thevariant protein can then be isolated from the cells by an appropriatepurification scheme using standard protein purification techniques. Manyof these techniques are described in detail below.

A protein is comprised of an amino acid sequence when the amino acidsequence is at least part of the final amino acid sequence of theprotein. In such a fashion, the protein may be a PAD polypeptide, avariant PAD polypeptide and/or have additional amino acid molecules,such as amino acid residues (contiguous encoded sequence) that arenaturally associated with it or heterologous amino acid residues/peptidesequences. Such a protein can have a few additional amino acid residuesor can comprise several hundred or more additional amino acids. A briefdescription of how various types of these proteins can be made/isolatedis provided below.

The variant proteins of the present invention can be attached toheterologous sequences to form chimeric or fusion proteins. Suchchimeric and fusion proteins comprise a variant protein operativelylinked to a heterologous protein having an amino acid sequence notsubstantially homologous to the variant protein. “Operatively linked”indicates that the variant protein and the heterologous protein arefused in-frame. The heterologous protein can be fused to the N-terminusor C-terminus of the variant protein.

A chimeric or fusion protein can be produced by standard recombinant DNAtechniques. For example, DNA fragments coding for the different proteinsequences are ligated together in-frame in accordance with conventionaltechniques. In another embodiment, the fusion gene can be synthesized byconventional techniques including automated DNA synthesizers.Alternatively, PCR amplification of gene fragments can be carried outusing anchor primers which give rise to complementary overhangs betweentwo consecutive gene fragments which can subsequently be annealed andre-amplified to generate a chimeric gene sequence (see Ausubel et al.,Current Protocols in Molecular Biology, 1992). Moreover, many expressionvectors are commercially available that already encode a fusion moiety(e.g., a GST protein). A variant protein-encoding nucleic acid can becloned into such an expression vector such that the fusion moiety islinked in-frame to the variant protein.

Polypeptides sometimes contain amino acids other than the 20 amino acidscommonly referred to as the 20 naturally occurring amino acids. Further,many amino acids, including the terminal amino acids, may be modified bynatural processes, such as processing and other post-translationalmodifications, or by chemical modification techniques well known in theart. Common modifications that occur naturally in polypeptides aredescribed in basic texts, detailed monographs, and the researchliterature, and they are well known to those of skill in the art.Accordingly, the variant peptides of the present invention alsoencompass derivatives or analogs in which a substituted amino acidresidue is not one encoded by the genetic code, in which a substituentgroup is included, in which the mature polypeptide is fused with anothercompound, such as a compound to increase the half-life of thepolypeptide (for example, polyethylene glycol), or in which theadditional amino acids are fused to the mature polypeptide, such as aleader or secretory sequence or a sequence for purification of themature polypeptide or a pro-protein sequence.

Known modifications include, but are not limited to, acetylation,acylation, ADP-ribosylation, amidation, covalent attachment of flavin,covalent attachment of a heme moiety, covalent attachment of anucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, demethylation,formation of covalent crosslinks, formation of cystine, formation ofpyroglutamate, formylation, gamma carboxylation, glycosylation, GPIanchor formation, hydroxylation, iodination, methylation,myristoylation, oxidation, proteolytic processing, phosphorylation,prenylation, racemization, selenoylation, sulfation, transfer-RNAmediated addition of amino acids to proteins such as arginylation, andubiquitination.

The present invention further provides fragments of the variant proteinsof the present invention, in addition to proteins and peptides thatcomprise and consist of such fragments, provided that such fragments actas an antigenic determinant and/or provide treatment for and/orprotection against PRRSV infections as provided by the presentinvention.

As used herein, a fragment comprises at least 8 or more contiguous aminoacid residues from a PAD polypeptide or variant protein.

The terms “fragment,” “derivative” and “homologue” when referring to thepolypeptides according to the present invention, means a polypeptidewhich retains essentially the same biological function or activity assaid polypeptide, that is, act as an antigenic determinant and/orprovide treatment for and/or protection against PRRSV infections. Suchfragments, derivatives and homologues can be chosen based on the abilityto retain one or more of the biological activities of a PAD polypeptide,that is, act as an antigenic determinant and/or provide treatment forand/or protection against PRRSV infections. Thus, a homologue includes apolypeptide from a different strain or genus that retains essentiallythe same biological function or activity as the PAD polypeptide. Thepolypeptide vaccines of the present invention may be recombinantpolypeptides, natural polypeptides or synthetic polypeptides, preferablyrecombinant polypeptides.

An “antigenic determinant” is, unless otherwise indicated, a moleculethat is able to elicit an immune response in a particular animal orspecies. Antigenic determinants include proteinaceous molecules, i.e.polyaminoacid sequences, polypeptides, fragments, derivatives orvariants that may include other moieties, for example, carbohydratemoieties, such as glycans, and/or lipid moieties.

Antigenic determinants of the present invention may also beheterologous, including antigenic determinants of neutralizing epitopesfrom other viruses, PRRSV strains or family, that cross-react withantibody or antiserum produced in response to a PAD of the presentinvention, for example, GP5-M heterodimers, and are able to elicit animmune response in a particular animal, such as a pig.

“M” as used herein refers to a matrix protein or polypeptide of PRRSV.The term “M” as used herein also includes fragment, derivatives orhomologs thereof that can form a heterodimer with a GP5 protein andprovide cross-reactivity with PRRSV strains.

“GP5” as used herein refers to a glycoprotein 5 of PRRSV. The term “GP5”as used herein also includes fragment, derivatives or homologs thereofthat can form a heterodimer with a M protein and providecross-reactivity with PRRSV strains. Thus, a homolog of GP5, forexample, from another arterivirus virus, is contemplated as part of theinvention. The position in the GP5 homolog that corresponds to position44 of GP5 in NA PRRSV strains or to position 46 of GP5 in EU PRRSVstrains can be determined by one skilled in the art and are alsoincluded as part of the invention.

The term “GP5-M heterodimer” as used herein also includes a GP5 proteinassociated with the M protein of PRRSV or any other protein or peptidethat alters the conformation of GP5 such that when administered to a pigprovides protection against PRRSV. One skilled in the art would be ableto test for conformational changes of GP5 using standard techniques andmethods, for example, using a monoclonal antibody that only recognizesthe GP5 protein when it is not in heterodimeric form. Thus, one aspectof the invention includes GP5 or M proteins from the same or fromdiffering strains or viruses, including but not limited to equinearteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), andsimian hemorrhagic fever virus (SHFV) family members. Thereforeaccording to the invention, chimeric GP5-M heterodimers may be employedas PAD, for example, for use in immunization protocols.

As used herein, the ectodomain of the GP5 protein is approximately 60-65amino acids in length includes a signal peptide and post-processing ashort N-terminal region of approximately 30 amino acids in length whichmay include N-glycosylation sites. See FIG. 1. As used herein, the term“hypervariable” region refers to a region of the ectodomain of the GP5protein, for example, amino acids 1 to 35 of GP5 in (NA) North Americanstrains of PRRSV and amino acids 1 to 37 of GP5 in (EU) European likePRRSV strains or of a GP5 homolog or equivalent thereof. Correspondingregions and positions of the ectodomain in other fragments, homologs orderivatives of GP5 can be determined for example by alignment and usedin the present invention. Also, contemplated as part of the inventionare mutations of one or more amino acids in the ectodomain of GP5 thatresult in the glycosylation of that amino acid. Thus, it may be possibleto generate a GP5 that has glycosylation in the ectodomain at a positionother than 44 in NA PRRSV strains or 46 in EU PRRSV strains that has thesame effect (protection against PRRSV infection). These variants mayalso be used in the present invention.

As used herein, the ectodomain of the M protein refers to the first 30amino acids of the N-terminus of the M protein or of a homolog orequivalent thereof. Corresponding regions and positions of theectodomain in other fragments, homologs or derivatives of M protein canbe determined for example by alignment and used in the presentinvention.

The phrase “biological sample” refers to a fluid or tissue of a mammal(e.g., a pig, rabbit, horse) that commmonly contains antibodies or viralparticles. Such components are known in the art and include, withoutlimitation, blood, plasma, serum, spinal fluid, lymph fluid, secretionsof the respiratory, intestinal or genitourinary tracts, tears, saliva,milk, white blood cells, and myelomas.

As used herein, an antibody is defined in terms consistent with thatrecognized within the art: they are multi-subunit proteins produced by amammalian organism in response to an antigen challenge. The antibodiesof the present invention include monoclonal antibodies and polyclonalantibodies, as well as fragments of such antibodies, including, but notlimited to, Fab or F(ab′)hd 2, and Fv fragments.

As used herein, the term “subunit” refers to a portion of the PRRSVwhich is itself antigenic, i.e., capable of inducing an immune responsein an animal. The term should be construed to include subunits which areobtained by both recombinant and biochemical methods.

As used herein, the term “multivalent” means a vaccine containing morethan one isolate from the PRRSV, whether from the same species (i.e.,different isolates of PRRSV) or from a different PRRSV. Even for a givengenus and species of PRRSV each isolate may share some antigens withother isolates (i.e., “common” antigens), while other antigens will beunique to that isolate. Because a multivalent vaccine provides a greatervariety of antigens to the host's immune system, the immune responsestimulated in the host is broader than that stimulated by only a singleisolate.

As used herein, the term “isolate” refers to a virus obtained from aspecific source. Isolate is used interchangeably with the term “strain”.

As used herein, the term “virulent” means an isolate that retains itsability to be infectious in an animal host.

As used herein, the term “inactivated” means a vaccine containing aninfectious organism that is no longer capable of replication and/orgrowth.

As used herein, the term “PRRSV” as used herein refers to all virusesbelonging to species PRRSV in the genus Arterivirus within the familyArteriviridae.

As used herein, the term “vaccine” as used herein refers to apharmaceutical composition comprising at least one immunologically PADthat induces an immunological response in an animal and possibly, butnot necessarily, one or more additional components that enhance theimmunological activity of said active component. A vaccine mayadditionally comprise further components typical to pharmaceuticalcompositions. The immunologically active component of a vaccine maycomprise complete live virus in either its original form or asattenuated virus in a so-called modified live vaccine or virusinactivated by appropriate methods in a so-called killed vaccine. Inanother form, the immunologically active component of a vaccine maycomprise appropriate elements of said viruses (subunit vaccines) wherebythese elements are generated either by destroying the whole organism orthe growth cultures of such viruses and subsequent purification stepsyielding in the desired structure(s), or by synthetic processes inducedby an appropriate manipulation of a suitable system such as, but notrestricted to, bacteria, insects, mammalian, or other species, plussubsequent isolation and purification procedures or by induction of saidsynthetic processes in the animal needing a vaccine by directincorporation of genetic material using suitable pharmaceuticalcompositions (polynucleotide vaccination). A vaccine may comprise one orsimultaneously more than one of the elements described above.

The terms “protecting”, “protection”, “protective immunity” or“protective immune response,” as used herein, are intended to mean thatthe host pig mounts an active immune response to the vaccine orpolypeptides of the present invention, such that upon subsequentexposure to the virus or a virulent viral challenge, the pig is able tocombat the infection. Thus, a protective immune response will decreasethe incidence of morbidity and mortality from subsequent exposure to thevirus among host pigs. Those skilled in the art will understand that ina commercial pig setting, the production of a protective immune responsemay be assessed by evaluating the effects of vaccination on the herd asa whole, e.g., there may still be morbidity and mortality in a minorityof vaccinated pigs. Furthermore, protection also includes a lessening inseverity of any gross or histopathological changes (e.g., lesions in thelung) and/or of symptoms of the PPRS disease, as compared to thosechanges or symptoms typically caused by the isolate in similar pigswhich are unprotected (i.e., relative to an appropriate control). Thus,a protective immune response will decrease the symptoms of PRRSV,including but not limited to a reduction in the clinical signs orsymptoms of PRRS comprising weight loss, decreased weight gain,lethargy, respiratory distress, “thumping” (forced expiration), fevers,roughened haircoats, sneezing, coughing, eye edema, conjunctivitis,gross lesions microscopic lung lesions, myocarditis, lymphadenitis,encephalitis and rhinitis compared to the control pig.

As used herein, the term “live virus” refers to a virus that retains theability of infecting an appropriate subject (as opposed to inactivated(killed) or subunit vaccines).

As used herein, “immunogenically effective amount” refers to an amount,which is effective in reducing, eliminating, treating, preventing orcontrolling the symptoms of the PRRSV infections, diseases, disorders,or condition.

In one embodiment, the present invention relates to a polypeptidecomprising a PAD of PRRSV, herein referred to as a PAD polypeptide. Thepresent inventors contemplate that the polypeptide may be a homologue, aderivative, or a variant of the PAD, or an immunologically active or afunctional fragment thereof. The polypeptide may be isolated,synthesized, or recombinantly expressed using the PAD-encoding nucleicacids described herein.

Examples of PADs of the present invention include but are not limited tothe amino acid sequences shown in FIGS. 1, 20, 21 and 22 (SEQ ID NOS:1-11 and 25-87). These PADs may be administered as fragments,polypeptides, proteins, or as a PRRSV having the desired glycosylationof the ectodomain of the GP5-M heterodimer according to the immunizationprotocols described herein. Further examples of nucleic acid moleculesof the present invention include, but are not limited to thepolynucleotide sequences that encode the polypeptide of (HLV013)MLGRCLTAGC CSQLPFLWCI VPFCLVALVN ANSNSGSHLQ LIYNLTLCEL NGTDWLKDKF (SEQID NO: 93) or the polypeptide of and HLV093 MLGRCLTACY CLRLLSLWCIVPFWFAVLVS ANSNSSSHLQ SIYKLTLCEL NGTEWLNERF (SEQ ID NO: 94).

The present invention also provides isolated and/or recombinant nucleicacids that encode a PAD polypeptide of the invention. According to anembodiment of the invention, the nucleotide sequence of a PAD encodes aneutralizing epitope of PRRS. In addition, it should be understood basedon the general state of the art that other equivalent sequences to thenucleotide or amino acid sequences of the PADs are covered by thepresent invention. For example, some deletions, insertions andsubstitutions in the amino acid sequence of the ectodomain of the GP5are covered by the present invention, unless such mutation abolishes theability of the PAD to induce the generation of neutralizing antibody.

The PAD-encoding nucleic acids of the invention are useful for severalpurposes, including the recombinant expression of the corresponding PADpolypeptides.

Nucleic acids of the invention include those that encode an entire PADas well as those that encode a subsequence of a PAD polypeptide. Forexample, the invention includes nucleic acids that encode a polypeptidewhich is not a full-length PAD, but nonetheless has protective antigenicactivity against PRRSV infection. The invention includes not onlynucleic acids that include the nucleotide sequences as set forth herein,but also nucleic acids that are substantially identical to, orsubstantially complementary to, the exemplified embodiments. Forexample, the invention includes nucleic acids that include a nucleotidesequence that is at least about 70% identical to one that is set forthherein, more preferably at least 75%, still more preferably at least80%, more preferably at least 85%, still more preferably at least 90%,and even more preferably at least about 95% identical to an exemplifiednucleotide sequence. The nucleotide sequence may be modified asdescribed previously, so long as the polypeptide encoded is capable ofinducing the generation of neutralizing antibodies.

The nucleic acids that encode a PAD polypeptide of the invention can beobtained using methods that are known to those of skill in the art.Suitable nucleic acids (e.g., cDNA, genomic, or subsequences) can becloned, or amplified by in vitro methods such as the polymerase chainreaction (PCR) using suitable primers, the ligase chain reaction (LCR),the transcription-based amplification system (TAS), the self-sustainedsequence replication system (SSR). A wide variety of cloning and invitro amplification methodologies are well-known to persons of skillExamples of these techniques and instructions sufficient to directpersons of skill through many cloning exercises are found in Berger andKimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology 152Academic Press, Inc., San Diego, Calif. (Berger); Sambrook et al. (1989)Molecular Cloning—A Laboratory Manual (2nd ed.) Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor Press, NY, (Sambrook et al.);Current Protocols in Molecular Biology, F. M. Ausubel et al., eds.,Current Protocols, a joint venture between Greene Publishing Associates,Inc. and John Wiley & Sons, Inc., (1994 Supplement) (Ausubel); Cashionet al., U.S. Pat. No. 5,017,478; and Carr, European Patent No.0,246,864. Examples of techniques sufficient to direct persons of skillthrough in vitro amplification methods are found in Berger, Sambrook,and Ausubel, as well as Mullis et al., (1987) U.S. Pat. No. 4,683,202;PCR Protocols A Guide to Methods and Applications (Innis et al., eds)Academic Press Inc. San Diego, Calif. (1990) (Innis); Amheim & Levinson(Oct. 1, 1990) C&EN 36-47; The Journal Of NIH Research (1991) 3: 81-94;(Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173; Guatelli et al.(1990) Proc. Natl. Acad. Sci. USA 87, 1874; Lomell et al. (1989) J.Clin. Chem., 35: 1826; Landegren et al., (1988) Science 241: 1077-1080;Van Brunt (1990) Biotechnology 8: 291-294; Wu and Wallace (1989) Gene 4:560; and Barringer et al. (1990) Gene 89: 117. Improved methods ofcloning in vitro amplified nucleic acids are described in Wallace etal., U.S. Pat. No. 5,426,039. Nucleic acids that encode the PADpolypeptide of the invention, or subsequences of these nucleic acids,can be prepared by any suitable method as described above, including,for example, cloning and restriction of appropriate sequences.

A nucleic acid encoding a PAD polypeptide may then be introduced intoeither a prokaryotic or eukaryotic host cell through the use of avector, plasmid or construct and the like to produce the PAD polypeptideof the invention. A typical expression cassette contains a promoteroperably linked to a nucleic acid that encodes the glycosyltransferaseor other enzyme of interest. The expression cassettes are typicallyincluded on expression vectors that are introduced into suitable hostcells, including for example, bacterial, insect, fungal, plant or animalcells. Either constitutive or regulated promoters can be used in thepresent invention. Promoters suitable for use in eukaryotic host cellsare well known to those of skill in the art. The expression vectors ofthe invention can be transferred into the chosen host cell by methodsknown to those of ordinary skill in the art including, for example,calcium phosphate transfection, DEAE-dextran mediated transfection,transvection, microinjection, cationic lipid-mediated transfection,electroporation, transduction, scrape loading, ballistic introduction,infection or other methods. (See Molecule Cloning: A Laboratory Manual,2^(nd) ed., Vol. 1-3, ed. Sambrook et al., Cold Spring Harbor LaboratoryPress (1989)). Transformed cells can be selected, for example, byresistance to antibiotics conferred by genes contained on the plasmids,such as the amp, gpt, neo and hyg genes.

A PAD polypeptide, homologue, fragments or other derivatives, orvariants thereof, or cells expressing it can be used as an antigen toproduce antibodies thereto. The present invention includes, for examplesmonoclonal and polyclonal antibodies, chimeric, single chain, as well asFab fragments. Thus, the present invention also encompasses a method ofgenerating antibodies directed against one or more PAD polypeptidesdescribed above comprising providing a polypeptide of the PAD or abiologically functional homologue or derivative or variant thereof andadministering the polypeptide to an animal subject in an amountsufficient to induce an immunological response to generate antibodiesdirected towards the PAD polypeptide. Thus, the invention includes amethod for generating antibodies against a protective antigenicdeterminant (PAD) of PRRSV that includes administering to an animal afirst GP5-M heterodimer, where the GP5 of the first GP5-M heterodimerhas glycosylation at position 44 of the GP5 of a North American (NA)PRRSV or glycosylation at position 46 of the GP5 of a European (EU)PRRSV. The method also includes administering to the animal a secondGP5-M heterodimer, where the GP5 of the second GP5-M heterodimer doesnot have glycosylation at position 44 of GP5 of a North American (NA)PRRSV or at position 46 of the GP5 of a European (EU) PRRSV. Theinventors also contemplate that amino acids of 51 and 53 in GP5 in NAand EU PRRSV respectively may be important for use as a PAD and believethat they may be involved in viral attachment and that VN antibodies mayreact with them. The PADs of the invention may be administered accordingto the immunization protocol described herein. In another aspect of theinvention, the animal is a non-human, for example, a rat, horse, cow,mouse, pig, sheep, rabbit, or chicken.

Thus, the invention provides antibodies that selectively bind to the PADpolypeptide, a derivative, a homologue or a variant as well as fragmentsthereof. Such antibodies may be used to quantitatively or qualitativelydetect the PAD polypeptide or variants as described previously.

Many methods are known for generating and/or identifying antibodies to agiven target peptide, such as a PAD polypeptide. Several such methodsare described by Harlow, Antibodies, Cold Spring Harbor Press, (1989).The full-length PAD polypeptide, derivative, homologue or variant orfragments or a fusion protein can be used.

For preparation of monoclonal antibodies, any technique known in the artwhich provides antibodies produced by continuous cell line cultures canbe used. Examples include various techniques, such as those in Kohler,G. and Milstein, C., Nature 256:495-497 (1975); Kozbor et al.,Immunology Today 4:72 (1983); (Cole et al., pg. 77-96 in MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, Inc. (1985). Monoclonalantibodies can be produced by hybridomas, which are immortalized celllines capable of secreting a specific monoclonal antibody. Theimmortalized cell lines can be created in vitro by fusing two differentcell types, usually lymphocytes, one of which is a tumor cell.

The anti-PAD antibodies may comprise polyclonal antibodies. Methods ofpreparing polyclonal antibodies are known to the skilled artisan.Polyclonal antibodies can be raised in a mammal, for example, by one ormore injections of an immunizing agent and, if desired, an adjuvant.Typically, the immunizing agent and/or adjuvant will be injected in themammal by multiple subcutaneous or intraperitoneal injections. Theimmunizing agent may include the PAD polypeptide, derivative, ahomologue or a variant as well as fragments or a fusion protein thereof.It may be useful to conjugate the immunizing agent to a protein known tobe immunogenic in the mammal being immunized. Examples of suchimmunogenic proteins include but are not limited to keyhole limpethemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsininhibitor. Examples of adjuvants which may be employed include Freund'scomplete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A,synthetic trehalose dicorynomycolate). The immunization protocol may beselected by one skilled in the art without undue experimentation.

In another embodiment of the present invention, a method is provided forpreparing a vaccine against PRRSV. In one aspect, the method comprisesproviding a PAD polypeptide, a derivative, a homologue or a variant orfragments thereof. Alternately, the method for preparing a vaccineagainst PRRSV may include mixing the PAD polypeptide with aphysiologically acceptable carrier or diluent. Generally, vaccines areprepared as injectables, in the form of aqueous solutions orsuspensions. Vaccines in an oil base are also well known such as forinhaling. Solid forms which are dissolved or suspended prior to use mayalso be formulated. Pharmaceutical or physiological carriers aregenerally added that are compatible with the active ingredients andacceptable for pharmaceutical use. Examples of such carriers include,but are not limited to, water, saline solutions, dextrose, or glycerol.Combinations of carriers may also be used. One of ordinary skill in theart would be familiar with pharmaceutically or physiologicallyacceptable carriers or diluents.

In view of the above, the present invention also provides for a vaccine.In another embodiment, there is provided a vaccine which includes atleast one PAD polypeptide, a derivative, a homologue or a variant orfragment thereof. In another aspect, the vaccine comprises a nucleicacid encoding a PAD polypeptide, a derivative, a homologue or a variantor fragment thereof.

The present invention provides for vaccines that are killed(inactivated), attenuated (live modified), subunit, DNA, or recombinantvector based. The invention provides in a further aspect a vaccine foruse in the protection of pigs against disease conditions resulting froma PRRSV infection. The vaccines of the present invention are generallyintended to be a prophylactic treatment which immunizes pigs againstdisease caused by virulent strains of PRRSV. However, the vaccines arealso intended for the therapeutic treatment of pigs already infectedwith a virulent strain of PRRSV.

The present inventors contemplate that PRRSV treatment and preventionmay be based on an entirely different theory than current vaccinestrategies, e.g. strategies involving mechanisms associated with eithercell mediated immunity (CMI) and/or virus neutralizing (VN) antibodies.The inventors believe that the PRRSV has a “glycan shield” that mayeither block or shield neutralizing epitopes (NE). The shield preventsthe humoral immune response from recognizing key neutralizing epitopescontaining asparagine-linked glycans or other sugar moieties, so thatthe neutralizing epitopes are unavailable for generation of neutralizingantibodies. The inventors also believe that PRRSV has a NE block glycanin some situations (FIG. 17). When a host “species jump” occurs by anRNA virus, neutralizing antibody (Nab) to the NE may be readily induced(FIG. 16). These first “species jump” trains with no glycans in block orshield positions are readily eliminated by Nab to NE.

As new host species become infected or quasispecies develop, the NEbecomes blocked (BNE) by glycan(s) in direct proximity (conservedregion) of the NE (FIG. 17), for example, the sequence of HLV013 in FIG.10. Subsequently, Nab is created to the BNE. Next a shield of glycans(SNE) evolves on emerging quasispecies in hypervariable region(s) inproximity of the NE. Thus, Nab may be slow to develop and/or beineffective against escape mutants containing both BNE and SNE (FIG.19).

If only the glycan shield is present e.g. rare wild type mutants, thenNab is induced to the NE (FIG. 19), for example, HLV093. See FIG. 11.This Nab protects against strains with only the glycan shield. Thus,strains with only a glycan shield are not maintained in the susceptiblehost population. The sequential immunization of wild type mutantspossessing no glycan shield (BNE [FIG. 17] followed by NE [FIG. 18])results in polyclonal Nab which protects against predominant emergingheterologous virus strains and provides cross-reactivity (FIG. 19).

Thus, viruses emerge by first forming a glycan block and then a glycanshield (FIG. 19). Heterologous Nab may be produced by first inoculatinga glycan blocked epitope (BNE) without a glycan shield followed by a NEwithout the glycan block which is referred to as reversed epitopeevolution immunization.

Thus, the present inventors believe that when a pig is exposed to aninitial and then a subsequent differing strain of PRRSV that is moreglycosylated in the hypervariable ectodomain of GP5, the pig's immunesystem only recognizes non-glycsoylated regions on GP5 and M in theneutralizing epitope and shared epitopes between the serotypes. As aconsequence, the immune system is unable to recognize new glycosylatedepitopes on PRRSV resulting in ineffective immunity.

The present inventors are first to recognize that this theory can beexploited for use in the development and administration of single ormultivalent PRRSV vaccines and PRRSV immunization schemes usingglycantyping of PRRSV isotypes. Thus, glycosylation patterns(glycantypes) of PRRSV may be used for initial grouping of PRRSVstrains.

According to the present invention, PRRSV strains within the NorthAmerican and European genotypes are grouped based on their glycosylationpatterns. This discovery is referred to by the inventors as aglycantyping scheme. Glycantyping is a more accurate means of discerningheterologous PRRSV strains as new strains emerge in the population thansequence homology of ORF5. The present inventors contemplate that thediscernment of glycosylation patterns can be used in single ormultivalent vaccines or in the development of vaccination schemes andprotocols. In one aspect, the strains are classified based on whetherthey are European or North American strains. In another aspect of typingthe PRRSV strains, the first letter is either EU (European like) or NA(North American like) to designate the genotype cluster. As used herein,EU refers to isotypes of PRRSV characterized by conserved glycans atposition 46, 53, or both in GP5. As used herein, NA refers to isotypesof PRRSV characterized by conserved glycans at position 44, 51, or bothin GP5. Each strain is given a number corresponding to the number ofglycosylation sites located in the ectodomain of GP5 amino acid sequenceshown in Table 7, but excludes highly conserved glycans located at aa44and 51 for NA strains and aa46 and 53 for EU strains. Thus, NA-0 refersto the ectodomain of GP5 of NA strain that has no glycan and EU-0 refersto the ectodomain of GP5 of an EU strain that has no glycan. Forexample, NA-1 refers to the ectodomain of GP5 of a North American strainthat has 1 glycan located on the ectodomain of GP5 excluding highlyconserved glycans located at aa44 and 51 for NA strains.

The present invention also contemplates that newly identified PRRSVstrains may be glycantyped using the above described methodology andaccordingly used in embodiments of the present invention. The inventorsalso contemplate that glycantyping schemes described herein may also beapplicable in treating or preventing other viruses that utilize a“glycan shield” to evade the immune system, for example, in designingimmunization protocols. New or known PRRSV strains can also be isolatedfrom the field using standard techniques and methods known in the art.

According to the invention, virulent or avirulent PRRSV may be used in avaccine or in an immunization protocol. The inventors have found thatthis method of administering PRRS viral strain with N-glycosylation inthe ectodomain of GP5, in particular a glycan at position 44 (or 46)depending on whether the GP5 mimics a North American or European PRRSVin the GP5-M heterodimer to vaccinate pigs is particularly capable ofpriming a pig's immune system to elicit a greater immune response whenfollowed by administration with a PRRSV strain having no glycosylatedamino acids in the GP5 ectodomain and subsequently challenged with aPRRSV having glycosylation ectodomain in its GP5 polypetpide. See Table6. This rational is based on the fact that glycans in the GP5hypervariable region may inhibit/delay a protective antibody response tothe PADs. Furthermore, it is believed that the absence of a glycan atposition 44 contributes to protection against heterologous strains ofthe virus. For example, a strain such as HLV093 that is deficient ofglycans in its neutralizing epitope in GP5 may be used to prime theimmune response prior to encountering other glycantypes of PRRSV. Foreexample, a strain such as HLV013 that is deficient of glycans in itshypervariable region (1-37) in GP5 may be used to prime the immuneresponse prior to encountering other glycantypes of PRRSV.

In one aspect of the immunization protocol against a PPRSV infection, avirus having a PAD of a GP5-M heterodimer of PRRSV of the presentinvention with glycosylation at position 44 of GP5 in a North Americanstrain is administered, followed by administration of a virus having aPAD of a GP5-M heterodimer of PRRSV of the present invention withoutglycosylation at position 44 of GP5 in a North American strain, and thenchallenged with a PRRSV having glycosylation in the neutralizing epitopeof GP5.

In another aspect, a virus having a PAD of a GP5-M heterodimer of PRRSVof the present invention with glycosylation at position 46 in GP5 in aEuropean strain is administered, followed by administration of a virushaving a PAD of a GP5-M heterodimer of PRRSV of the present inventionwithout glycosylation at position 46 in GP5 in a European strain, andthen challenged with a PRRSV having glycosylation in the neutralizingepitope of GP5.

In one aspect of the immunization protocol against a PPRSV infection, aPAD comprising a GP5-M heterodimer of PRRSV of the present inventionwith glycosylation at position 44 of GP5 in a North American strain isadministered, followed by administration of a PAD comprising a GP5-Mheterodimer of PRRSV of the present invention without glycosylation atposition 44 of GP5 in a North American strain, and then challenged witha strain of PRRSV having glycosylation in the neutralizing epitope ofGP5. In another aspect, a PAD comprising a GP5-M heterodimer of PRRSV ofthe present invention with glycosylation at position 46 of a GP5 in aEuropean strain is administered, followed by administration of a PADcomprising a GP5-M heterodimer of PRRSV of the present invention withoutglycosylation at position 46 of GP5 in a European strain, and thenchallenged with a strain of PRRSV having glycosylation in theneutralizing epitope of GP5.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-35 in the NA PRRSV GP5 protein. In another aspect, aPAD of GP5 may have a glycan at position 44 in the NA PRRSV GP5 protein.In another aspect, a PAD of GP5 may have a glycan at position 44 in theNA PRRSV GP5 and have glycans present or absent in amino acids 1-35 inthe NA PRRSV GP5 protein, for example, as found in some NA PRRSVstrains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-35 in the NA PRRSV GP5 protein. In anotheraspect, a PAD of GP5-M heterodimer may have a glycan at position 44 inthe NA PRRSV GP5 protein. In another aspect, a PAD of GP5-M heterodimermay have a glycan at position 44 in the NA PRRSV GP5 and have glycanspresent or absent in amino acids 1-35 in the NA PRRSV GP5 protein, forexample, as found in some NA PRRSV strains.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-37 in the EU PRRSV GP5 protein, as found in Lelystad.In another aspect, a PAD of GP5 may have a glycan at position 46 in theEU PRRSV GP5 protein. In another aspect, a PAD of GP5 may have a glycanat position 46 in the EU PRRSV GP5 and have glycans present or absent inamino acids 1-37 in the EU PRRSV GP5 protein, for example, as found insome EU PRRSV strains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-37 in the EU PRRSV GP5 protein, as foundin Lelystad. In another aspect, a PAD of GP5-M heterodimer may have aglycan at position 46 in the EU PRRSV GP5 protein. In another aspect, aPAD of GP5-M heterodimer may have a glycan at position 46 in the EUPRRSV GP5 and have glycans present or absent in amino acids 1-37 in theEU PRRSV GP5 protein, for example, as found in some EU PRRSV strains.

The present immunization process against PRRSV is advantageous in thatit results in the generation of high levels of neutralizing antibodiesin an early antibody response when challenged with PRRSV of variousstrains that provides heterologous reactivity. It is believed thatimmunization protocols described herein may be applicable to thetreatment and prevention of other viral infections, including, but notlimited to HW and influenza.

Thus, strains including and similar to HLV013 may or may not providedirect protection against all other glycantypes but rather indirectprotection by readying the immune system to progressively encounterPRRSV PADs with varying degrees of glycan masking. By contrast,subsequent inoculation of PADs of different strains similar to HLV093 inglycosylation of the hypervariable ectodomain of GP5 may provide accessto important neutralizing epitopes in all PRRSV strains, such as thosemore glycosylated in the hypervariable ectodomain of GP5. In this way,the glycantyping of PRRSV creates a ranking or order or combination ofPRRSV administration effective in generating an immune response tomultiple PRRSV. In one aspect of the present invention, multiple GP5-Mheterodimers (glycantypes) may be needed to induce widespread protectionagainst a variety of PRRSV strains.

Without wishing to be bound by this theory, the present inventorsbelieve that all immunogens representing the various glycantypes of GP5may need to be given together due to the concept of “original antigenicsin” (OAS) where the antibody response elicited in response to a secondviral infection reacts more strongly than the original variantinfection. Thus, the present inventors contemplate the pig's immunesystem can be primed with a single PAD or immunization with multiple PADto obtain a broader and more reactive immune response than doesimmunization with a single PAD. The use of a multivalent vaccinestrategy may circumvent original antigenic sin. Thus, according to theinvention, multiple PRRSV strains or PAD may be administeredsimultaneously or sequentially. For treatment of PRRSV or inducement ofprotective antibody to all epitopes of PAD, pigs may require exposure tomultiple GP5, M, or GP5-M heterodimer glycantypes.

In one embodiment of the invention, a method of identifying GP5-Mheterodimers that elicit protection against PRRSV is provided. Thismethod also includes fragments, derivatives, or homologs of the GP5 andM protein or GP5-M heterodimers. In one aspect, the method comprisesadministering to a test pig a first GP5-M heterodimer, where the GP5 hasglycosylation at position 44 of the GP5 of a North American (NA) porcinereproductive and respiratory syndrome virus (PSSRV) or glycosylation atposition 46 of the GP5 of a European (EU) PRRSV. The administration ofthe first GP5-M heterodimer to the test pig is followed byadministration of a second GP5-M heterodimer, where the GP5 of thesecond GP5-M heterodimer does not have glycosylation at position 44 ofGP5 of a North American (NA) PRRSV or at position 46 of the GP5 of aEuropean (EU) PRRSV. The test and control pigs are subsequentlychallenged with an infectious amount of a virus that causes PRRS, forexample, Lelystad. One skilled in the art would be familiar with thePRRS strains that cause PRRS and the route and dosage necessary toachieve infection. The method also includes determining whether thefirst and second administered GP5-M heterodimers are effective inprotecting a pig against the challenge PRRSV.

Various methods and techniques for determining whether the GP5-Mheterodimers provided protection against PRRSV infection are known tothose skilled in the art, including but not limited to, observing adifference between the test and control pig in the symptoms of PRRS, forexample, the clinical signs or symptoms of PRRS comprising weight loss,decreased weight gain, lethargy, respiratory distress, “thumping”(forced expiration), fevers, roughened haircoats, sneezing, coughing,eye edema, conjunctivitis, gross lesions microscopic lung lesions,myocarditis, lymphadenitis, encephalitis and rhinitis. A decrease in anyof the symptoms of PRRS observed in the test pig compared to the controlpig indicates that the first and second administered GP5-M heterodimersprovide a degree of protection against PRRS. Similar symptoms or anincrease in any of the symptoms of PRRS observed in the test pigcompared to those observed in the control pig indicate that the firstand second administered GP5-M heterodimers do not provide protectionagainst PRRS.

In another aspect, determining whether the GP5-M heterodimers providedprotection against PRRSV infection includes determining the presence orabsence of challenge PRRSV in the test pig by electron microscopy orantibody or assays such as the fluorescent focusing neutralizing (FFN)test or Western blot assay for the heterodimer may be used to give anindication of heterologous antibody production and protection. Thepresence of the challenge PRRSV indicates that the first and secondadministered GP5-M heterodimers are not effective in protecting againstPRRS and the absence of the challenge PRRSV indicates that the first andsecond administered GP5-M heterodimers are effective in protectingagainst PRRS.

The present inventors also contemplate that the GP5-M heterodimers ofthe present invention may be delivered using various vectors andviruses, for example, PRRSV. Thus, another aspect of the inventionincludes a method for identifying viruses that elicit protection againstPRRSV. These identified GP5-M heterodimers or viruses may be used in anPRRSV immunization protocol or vaccine. For example, a PRRSV comprisinga GP5-M heterodimer with N-glycosylation in the ectodomain of GP5, inparticular a glycan at position 44 for a NA PRRSV or 46 for a EU PRRSVmay be administered to a pig. The method also includes administering aNA or EU PRRSV strain having no glycosylated amino acids at position 44or 46 in the GP5. To determine if the viruses provide protection a pigadministered these “test” viruses may be challenged with a PRRSV, or anyvirus causing PRRS, and any PRRS symptoms observed and compared to acontrol pig that receive the challenge virus to determine if the “test”virus provides PRRSV protection.

In another aspect, a method of the invention includes identifying avirus or PAD that elicits protection against PRRSV for use in animmunization protocol or vaccine by administering fragments,derivatives, or homologs of GP5 having a glycan at position 44 for a NAPRRSV or 46 for a EU PRRSV as a heterodimer, for example, with a Mprotein of PRRSV followed by administering a GP5 heterodimer that has noglycosylated amino acids at position 44 or 46 in the GP5. To determineif the PADs provide protection a pig administered these “test” PAD maybe challenged with a PRRSV, for example, Lelystad or any virus causingPRRS, and observing any PRRS symptoms and comparing the symptoms to acontrol pig that receive the challenge virus to determine if the “test”PADs provides PRRSV protection. Protection may also be determined usingan incidence of morbidity and mortality.

The present inventors contemplate that any combination of killed(inactivated) PRRSV, attenuated (live modified) PRRSV, subunit, DNA, orrecombinant vector based having a GP5, M, or GP5-M heterodimer may beglycantyped and used in the progressive or sequential or combinatorialimmunization protocol or scheme described herein. In one aspect, theimmunization protocol or scheme induces antibodies to the PAD.

The present inventors contemplate that European like PRRSV strains maybe analogously glycantyped (Table 7) and used in an immunizationprotocol for pigs as described for the American like PRRSV.

According to the present invention, one embodiment of a PRRS vaccineincludes an attenuated PRRSV with a GP5, M, or GP5-M heterodimer asdescribed herein. The property of an attenuated strain to inducePRRS-associated disease conditions as described above are significantlyreduced or completely absent if the strain is a live attenuated virus.Therefore, it is desirable that particular live PRRSV vaccines comprisean attenuated PRRSV strain that generates an immune response to the GP5,M, or heterodimer of GP5-M of the attenuated PRRSV strain withoutcausing disease.

Methods for making attenuated viruses are well known in the art andinclude such methods as serial passage in cell culture on a suitablecell line or chemical mutagenesis. For example, attenuated variants ofPRRSV may be produced by serial passage of the virus on a cell line, forexample, Marc 145, CL2621, MA-104 cells, or porcine alveolar macrophagesfor between about 10 and 100 passages so that mutations accumulate thatconfer attenuation on the strain. Serial passaging refers to theinfection of a cell line with a virus isolate, the recovery of the viralprogeny from the host cells, and the subsequent infection of host cellswith the viral progeny to generate the next passage. During passage onthe cell line, the virus loses its ability to cause disease in the pig,e.g., becomes apathogenic or non-pathogenic, while maintaining itsability to replicate in the pig and produce a protective immuneresponse.

Therefore, to make a vaccine, the attenuated PRRSV isolate is grown incell culture on a suitable cell line, i.e., Marc 145, CL2621 or MA-104cells, to titers sufficient for producing a vaccine. The PRRSV isharvested according to methods well known in the art. For example, thevirus may be removed from cell culture and separated from cellularcomponents, typically by well known clarification procedures, e.g.,centrifugation, and may be further purified as desired using procedureswell known to those skilled in the art. The PRRSV may then beconcentrated, frozen, and stored at −70° C. or freeze-dried and storedat 4° C.

The isolation of an attenuated virus may be followed by a sequenceanalysis of its genome to determine the basis for the attenuatedphenotype. This is accomplished by sequencing the viral DNA andidentifying nucleotide changes in the attenuated isolate relative to thegenomic sequence of a control virus. Therefore, the molecular changesthat confer attenuation on a virulent PRRSV strain can be characterized.

One embodiment of the invention provided herein, includes theintroduction of sequence changes at any of the positions alone or incombination, in order to generate attenuated virus progeny in knownPRRSV strains or those yet to be identified and isolated. Viral genomeswith such alterations can be produced by any standard recombinant DNAtechniques known to those skilled in the art (Ausubel et al., CurrentProtocols in Molecular Biology, Greene Publishing Associates & WileyInterscience, New York, 1989) for introduction of nucleotide changesinto cloned DNA. A genome may then be ligated into an appropriate vectorfor transfection into host cells for the production of viral progeny.

The PRRSV prior to vaccination is mixed to an appropriate dosage and mayinclude a pharmaceutically acceptable carrier, such as a saline solutionand/or an adjuvant, such as aluminum hydroxide. Thus, PRRSV vaccines ofthe invention may include an immunogenically effective amount of one ormore attenuated PRRSV as described herein.

The attenuated virus composition may be introduced into a pig, with aphysiologically acceptable vehicle and/or adjuvant. Useful vehicles arewell known in the art, and include, e.g., water, buffered water, saline,glycine, hyaluronic acid and the like. The resulting aqueous solutionsmay be packaged for use as is, or lyophilized, the lyophilizedpreparation being rehydrated prior to administration, as mentionedabove. The compositions may contain pharmaceutically acceptableauxiliary substances as required to approximate physiologicalconditions, such as pH adjusting and buffering agents, tonicityadjusting agents, wetting agents and the like, for example, sodiumacetate, sodium lactate, sodium chloride, potassium chloride, calciumchloride, sorbitan monolaurate, triethanolamine oleate, and the like.

Administration of the live attenuated viruses disclosed herein may becarried out by any suitable means, including both parenteral injection(such as intraperitoneal, subcutaneous, or intramuscular injection), andby topical application of the virus (typically carried in thepharmaceutical formulation) to an airway surface. Topical application ofthe virus to an airway surface can be carried out by intranasaladministration (e.g. by use of dropper, swab, or inhaler which depositsa pharmaceutical formulation intranasally). Topical application of thevirus to an airway surface can also be carried out by inhalationadministration, such as by creating respirable particles of apharmaceutical formulation (including both solid particles and liquidparticles) containing the virus as an aerosol suspension, and thencausing the subject to inhale the respirable particles. Methods andapparatus for administering respirable particles of pharmaceuticalformulations are well known, and any conventional technique can beemployed. As a result of the vaccination the host becomes at leastpartially or completely immune to PRRSV infection of the serotypesadministered, or resistant to developing moderate or severe PRRSVinfection.

In another embodiment, the attenuated PRRSV of one particular strainhaving a desired PADs as described herein can be combined withattenuated viruses of other strains of PRRSV having the desired PADs asdescribed herein to achieve protection against multiple PRRSV. Accordingto the present invention, the different PRRSVs may be administeredsequentially or progressively or alternately administered simultaneouslyin an admixture. Sequential or progressive administration of the vaccinecompositions of the invention may be required to elicit sufficientlevels of immunity to multiple PRRSV strains. Single or multipleadministration of the vaccine compositions of the invention can becarried out. Multiple administration may be required to elicitsufficient levels of immunity. Levels of induced immunity can bemonitored by measuring amount of neutralizing secretory and serumantibodies, and dosages adjusted or vaccinations repeated as necessaryto maintain desired levels of protection. The property of an attenuatedstrain to induce PRRS-associated disease conditions as described aboveare significantly reduced or completely absent if the strain is in aninactivated form.

According to the present invention, one embodiment of a PRRSV vaccineincludes an inactivated (killed) PRRSV with a GP5, M, or GP5-M proteinheterodimer. The property of an inactivated strain to inducePRRS-associated disease conditions as described above are significantlyreduced or completely absent if the strain is inactivated (killed).Inactivation of a PRRSV strain may be accomplished by a variety ofmethods including freeze-thawing, chemical treatment (for example,treatment with thimerosal or formalin), sonication, radiation, heat orany other convention means sufficient to prevent replication or growthof the virus while maintaining the immunogenicity of the PRRSV strain.

The inactivated vaccine is made by methods well known in the art. Forexample, once the virus is propagated to high titers, it would bereadily apparent by those skilled in the art that the virus antigenicmass could be obtained by methods well known in the art. For example,the PRRSV antigenic mass may be obtained by dilution, concentration, orextraction. The PRRSV may be inactivated by treatment with formalin orwith binary ethyleneimine (BEI), both methods are well known to thoseskilled in the art. For example, inactivation of a PRRSV strain byformalin may be performed by mixing the PRRSV suspension with 37%formaldehyde to a final formaldehyde concentration of 0.05%. ThePRRSV-formaldehyde mixture is mixed by constant stirring forapproximately 24 hours at room temperature. The inactivated PRRSVmixture is then tested for residual live virus by assaying for growth ona suitable cell line, for example, Marc 145, CL2621 or MA-104 cells.

Inactivation of a PRRSV strain by BEI may be performed, for example, bymixing the PRRSV suspension of the present invention with 0.1 M BEI(2-bromo-ethylamine in 0.175 N NaOH) to a final BEI concentration of 1mM. The PRRSV-BEI mixture is mixed by constant stirring forapproximately 48 hours at room temperature, followed by the addition of1.0 M sodium thiosulfate to a final concentration of 0.1 mM. Mixing iscontinued for an additional two hours. The inactivated PRRSV mixture istested for residual live PRRSV by assaying for growth on a suitable cellline, for example, Marc 145 cells. The aforementioned inactivated PRRSVof the present invention may be mixed with any one of thepharmaceutically acceptable adjuvants or physiological carriers forformulating inactivated virus vaccines to the appropriate dosage level.Suitable formulations and modes of administration of the killed PRRSVvaccine are described below.

In one embodiment, a PRRSV vaccine of the present invention may be asubunit vaccine. In one aspect, the subunit is a GP5, M, or GP5-Mheterodimer of PRRSV. Viral subunits may be obtained from PRRSV usingbiochemical methods or they can be expressed by recombinant means insuitable cells, for example, eukaryotic cells. Methods of expressingviral subunits are common in the art. For example, methods of expressingviral subunits are described in the following articles and in thereferences cited therein: Possee, 1986, Virus research 5:43; Kuroda etal., 1986, EMBO J. 5: 1359; Doerfler, 1986, Curr. Topics Microbiol.Immunol. 131:51; Rigby, 1983, J. Gen. Virol. 64:255; Mackett et al.,1985, In: DNA Cloning, A Practical Approach, Vol II, Ed. D. M. Glover,IRL Press, Washington, D.C.; Rothestein, 1985, In: DNA Cloning, APractical Approach, Supra; Kinney et al., 1988, J. Gen. Virol. 69:3005;Panical et al., 1983, Proc. Natl. Acad. Sci. USA 80:5364; Small et al.,1985, In: Vaccinia Viruses as Vectors for Vaccine Antigens, pp. 175-178,Ed. J. Quinnan, Elsevier, N.Y.

In the practice of one embodiment of this invention, the GP5, M, orGP5-M heterodimer subunit may be produced in vitro by recombinanttechniques in large quantities sufficient for use in a subunit vaccine.

In another aspect, the GP5, M, or GP5-M heterodimer subunit may beexpressed by a recombinant vector, viral vector, or virus. In anotheraspect, the recombinant vector, viral vector, or virus expressing thesubunit may itself serve as a vaccine component acting as a as anantigen or an adjuvant and eliciting or enhancing the pig's immuneresponse to a GP5, M, or GP5-M protein heterodimer alone.

In a further embodiment of the present invention, the vaccine comprisesa recombinant virus vector containing a nucleic acid encoding theantigen of a GP5, M, or GP5-M heterodimer or immunogenic fragmentthereof from a PRRSV strain. Suitable recombinant virus vectors includebut are not limited to live adenovirus, poxvirus, baculovirus,pseudorabies virus (PRV), Venezuelan equine encephalitis (VEE) vectorssuch as strains V3526 or TC-83, and viral replicon particles (VRPs)derived from VEE, equine arteritis virus (EAV), or transmissiblegastroenteritis virus (TGE).

The recombinant virus of the present invention may also contain multiplecopies of one glycantype of a GP5, M, or GP5-M heterodimer subunit.Alternatively, the recombinant virus may contain more than one GP5, M,or GP5-M heterodimer subunit glycantype, so that the virus may expresstwo or more differing GP5, M, or GP5-M heterodimer subunits. In oneaspect, the GP5, M, or GP5-M heterodimer subunits may vary inglycosylation of the ectodomain of the GP5 protein.

In the construction of the virus vector of the present invention, theGP5, M, or GP5-M protein heterodimer subunit sequence is preferablyinserted in a viral strain under the control of an expression controlsequence in the virus itself. The techniques employed to insert the GP5,M, or GP5-M heterodimer subunit sequence into the viral vector and makeether alterations in the viral DNA, e.g., to insert linker sequences andthe like, are known to one of skill in the art. See, e.g., T. Maniatiset al, “Molecular Cloning. A Laboratory Manual”, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y. (1982). Thus, given the disclosurescontained herein the construction of suitable virus expression vectorsfor expression of a GP5, M, or GP5-M heterodimer subunit protein iswithin the skill of the art. The recombinant virus itself, constructedas described above, may be used directly as a vaccine component.According to this embodiment of the invention, the recombinant virus,containing the GP5, M, or GP5-M heterodimer subunit, is introduceddirectly into the subject pig by vaccination. The recombinant virus,when introduced into a subject pig directly, infects the pig's cells andproduces the GP5, M, or GP5-M heterodimer subunit in the pig's cells.

To make a recombinant virus vector that expresses the GP5, M, or GP5-Mheterodimer antigen or immunogenic fragment thereof, a cDNA encoding theGP5, M, or GP5-M heterodimer antigen or immunogenic fragment thereof isinserted into the genome of a virus vector, for example, liveadenovirus, poxvirus, baculovirus, pseudorabies virus (PRV), Venezuelanequine encephalitis (VEE) vectors such as strains V3526 or TC-83, andviral replicon particles (VRPs) derived from VEE, equine arteritis virus(EAV), or transmissible gastroenteritis virus (TGE). Recombinant viralvectors can be produced by any standard recombinant DNA techniques knownto those skilled in the art (Ausubel et al., Current Protocols inMolecular Biology, Greene Publishing Associates & Wiley Interscience,New York, 1989) for introduction of nucleotide changes into cloned DNA.A viral genome may then be ligated into an appropriate vector fortransfection into host cells for the production of viral progeny.

For any of the aforementioned recombinant virus vectors, the cDNAencoding the GP5, M, or GP5-M heterodimer antigen or immunogenicfragment thereof is operably linked to a eukaryote promoter at the 5′end of the cDNA encoding the antigen and an eukaryote termination signaland poly(A) signal at the 3′ end of the cDNA encoding the antigen. Asused herein, the term “operably linked” means that the polynucleotide ofthe present invention (as a cDNA molecule) and a polynucleotide (DNA)containing an expression control sequence, e.g., transcription promoterand termination sequences, are situated in a vector or cell such thatexpression of the antigen encoded by the cDNA is regulated by theexpression control sequence. Methods for cloning DNA such as the cDNAencoding the GP5, M, or GP5-M heterodimer antigen or immunogenicfragment thereof and operably linking DNA containing expression controlsequences thereto are well known in the art. Examples of promoterssuitable for expressing the GP5, M, or GP5-M heterodimer antigen orimmunogenic fragment thereof in the recombinant virus vectors are thecytomegalovirus immediate-early (CMV) promoter, the Rous sarcoma viruslong terminal repeat (RSV-LTR) promoter, the simian virus 40 (SV40)immediate-early promoter, and inducible promoters such as themetallothionein promoter. An example of a DNA having a termination andpoly(A) signal is the SV40 late poly(A) region. Another example of aviral expression system suitable for producing the antigen is theSindbis Expression system available from Invitrogen. The use of thesecommercially available expression vectors and systems are well known inthe art.

In an embodiment further still of the present invention, the vaccine isprovided as a nucleic acid or DNA molecule vaccine that elicits anactive immune response in the pig. The DNA molecule vaccine consists ofDNA having a nucleic acid sequence which encodes the GP5, M, or GP5-Mheterodimer antigenic determinant or immunogenic fragment thereof. Thenucleic acid encoding the GP5, M, or GP5-M heterodimer antigenicdeterminant or immunogenic fragment thereof is operably linked at ornear the start codon for the GP5, M, or GP5-M heterodimer antigenicdeterminant to a promoter that enables transcription of the GP5, M, orGP5-M heterodimer antigenic determinant or immunogenic fragment thereoffrom the nucleic acid when the nucleic acid is inoculated into the cellsof the pig. Preferably, the DNA molecule is in a plasmid. Promoters thatare useful for DNA vaccines are well known in the art and include, butare not limited to, the RSV LTR promoter, the CMV immediate earlypromoter, and the SV40 T antigen promoter. In one aspect, the nucleicacid be operably linked at or near the termination codon of the sequenceencoding the GP5, M, or GP5-M heterodimer antigenic determinant orimmunogenic fragment thereof to a nucleic acid fragment comprising atranscription termination signal and poly(A) recognition signal. The DNAvaccine is provided to the pig in an accepted pharmaceutical carrier orin a lipid or liposome carrier similar to those disclosed in U.S. Pat.No. 5,703,055 to Felgner. The DNA vaccine can be provided to the pig bya variety of methods such as intramuscular injection, intrajetinjection, or biolistic bombardment. Making DNA vaccines and methods fortheir use are provided in U.S. Pat. Nos. 5,589,466 and 5,580,859, bothto Felgner. Finally, a method for producing pharmaceutical grade plasmidDNA is taught in U.S. Pat. No. 5,561,064 to Marquet et al.

Therefore, using any suitable methods including those mentioned above,DNA vaccines that express the GP5, M, or GP5-M heterodimer antigen orimmunogenic fragment thereof are used to immunize pigs against PRRSV.The advantage of the DNA vaccine is that the DNA molecule isconveniently propagated as a plasmid which is a simple and inexpensivemeans for producing a vaccine, and since the vaccine is not live, manyof the regulatory issues associated with live recombinant virus vectorvaccines are not an issue with DNA vaccines. One skilled in the artwould appreciate that the DNA vaccine of the present invention cancomprise synthetically produced nucleic acids which are made by chemicalsynthesis methods well known in the art.

In an embodiment further still of the present invention, the vaccineconsists of the isolated and purified GP5, M, or GP5-M heterodimerantigen or immunogenic fragment thereof. Preferably, the GP5, M, orGP5-M heterodimer antigen or immunogenic fragment thereof is produced ina recombinant bacterium or eukaryote expression vector which producesthe antigen which is isolated and purified to make the vaccine. Forexample, the GP5, M, or GP5-M heterodimer antigen or immunogenicfragment thereof is produced in a microorganism such as bacteria, yeast,or fungi; in a eukaryote cell such as a mammalian or an insect cell; or,in a recombinant virus vector such as adenovirus, poxvirus, herpesvirus,Simliki forest virus, baculovirus, bacteriophage, sindbis virus, sendaivirus, live Venezuelan equine encephalitis (VEE) vectors such as strainsV3526 or TC-83, and viral replicon particles (VRPs) derived from VEE,equine arteritis virus (EAV), or transmissible gastroenteritis virus(TGE). Suitable bacteria for producing the GP5, M, or GP5-M heterodimerantigen or immunogenic fragment thereof include Escherichia coli,Bacillus subtilis, or any other bacterium that is capable of expressingheterologous polypeptides. Suitable yeast types for expressing the GP5,M, or GP5-M heterodimer antigen or immunogenic fragment thereof includeSaccharomyces cerevisiae, Schizosaccharomyces pombe, Candida, or anyother yeast capable of expressing heterologous polypeptides. Methods forusing the aforementioned bacteria, recombinant virus vectors, eukaryotecells to produce antigens for vaccines are well known in the art.

To produce the vaccine consisting of the GP5, M, or GP5-M heterodimerantigen or immunogenic fragment thereof, the nucleic acid encoding theGP5, M, or GP5-M heterodimer antigen or immunogenic fragment thereof isin a plasmid and the nucleic acid is operably linked to a promoter whicheffects the expression of the GP5, M, or GP5-M heterodimer antigen orimmunogenic fragment thereof in a microorganism. Suitable promotersinclude, but are not limited to, T7 phage promoter, T3 phage promoter,beta-galactosidase promoter, and the Sp6 phage promoter. Expression ofthe GP5, M, or GP5-M heterodimer antigenic determinant or immunogenicfragment thereof in a microorganism enables the GP5, M, or GP5-Mheterodimer antigenic determinant to be produced using fermentationtechnologies which are used commercially for producing large quantitiesof recombinant antigenic polypeptides. Methods for isolating andpurifying antigens are well known in the art and include methods such asgel filtration, affinity chromatography, ion exchange chromatography, orcentrifugation.

To facilitate isolation of the GP5, M, or GP5-M heterodimer antigenicdeterminant or immunogenic fragment thereof, a fusion polypeptide may bemade wherein the GP5, M, or GP5-M heterodimer or immunogenic fragmentthereof is linked to another polypeptide which enables isolation byaffinity chromatography. Preferably, a fusion polypeptide is made usingone of the expression systems infra. For example, the cDNA nucleic acidsequence encoding the GP5, M, or GP5-M heterodimer antigenic determinantor immunogenic fragment thereof is linked at either the 5′ end or 3′ endto a nucleic acid encoding a polypeptide. The nucleic acids are linkedin the proper codon reading frame to enable production of a fusionpolypeptide wherein the amino and/or carboxyl terminus of the GP5, M, orGP5-M heterodimer antigenic determinant or portion thereof is fused to apolypeptide which allows for the simplified recovery of the antigen as afusion polypeptide.

An example of a prokaryote expression system for producing the GP5, M,or GP5-M heterodimer antigenic determinant or immunogenic fragmentthereof for use in vaccines is the Glutathione S-transferase (GST) GeneFusion System available from Amersham Pharmacia Biotech, Piscataway,N.J., which uses the pGEX-4T-1 expression vector plasmid. The cDNAencoding the GP5, M, or GP5-M heterodimer antigenic determinant orimmunogenic fragment thereof is fused in the proper codon reading framewith the DNA encoding GST. The GST part of the fusion polypeptide allowsthe rapid purification of the fusion polypeptide using glutathioneSepharose 4B affinity chromatography. After purification, the GSTportion of the fusion polypeptide can be removed by cleavage with asite-specific protease such as thrombin or factor Xa to produce anantigenic determinant free of the GST polypeptide. The GP5, M, or GP5-Mheterodimer antigenic determinant or immunogenic fragment thereof freeof the GST polypeptide is produced by a second round of glutathioneSepharose 4B affinity chromatography.

Another method for producing a vaccine comprising the GP5, M, or GP5-Mheterodimer antigenic determinant or immunogenic fragment thereof is amethod which links in-frame with the cDNA encoding the antigenicdeterminant, DNA codons that encode polyhistidine. The polyhistidinepreferably comprises six histidine residues which allows purification ofthe fusion polypeptide by metal affinity chromatography, preferablynickel affinity chromatography. To produce the GP5, M, or GP5-Mheterodimer antigenic determinant or immunogenic fragment thereof freeof the polyhistidine, a cleavage site such as an enterokinase cleavagesite is fused in the proper reading frame between the codons encodingthe polyhistidine and the codons encoding the antigen. The antigen freeof the polyhistidine is made by removing the polyhistidine by cleavagewith enterokinase. The antigen free of the polyhistidine is produced bya second round of metal affinity chromatography which binds the freepolyhistidine. See Motin et al. Infect. Immun. 64: 4313-4318 (1996). TheXpress System, available from Invitrogen, Carlsbad, Calif., is anexample of a commercial kit which is available for making and thenisolating polyhistidine-polypeptide fusion protein.

Immunogenic compositions including vaccines may be prepared in a varietyof formulations, for example, injectables, liquid solutions oremulsions. The immunogens, for example, GP5, M, or GP5-M proteinheterodimer may be mixed with pharmaceutically acceptable excipientswhich are compatible with the immunogens. Such excipients may includewater, saline, dextrose, glycerol, ethanol, and combinations thereof.The immunogenic compositions and vaccines may further contain auxiliarysubstances, such as wetting or emulsifying agents, pH buffering agents,or adjuvants to enhance the effectiveness thereof.

Immunogenic compositions and vaccines may be administered parenterally,by injection subcutaneously or intramuscularly or in any other suitablemanner. The immunogenic preparations and vaccines are administered in amanner compatible with the dosage formulation, and in such amount aswill be therapeutically effective, immunogenic and protective. Thequantity to be administered depends on the subject to be treated,including, for example, the capacity of the immune system of theindividual to synthesize antibodies, and, if needed, to produce acell-mediated immune response. Precise amounts of active ingredientrequired to be administered depend on the judgment of the practitioner.However, suitable dosage ranges are readily determinable by one skilledin the art and may be of the order of micrograms of the immunogens.Suitable regimes for initial administration and booster doses are alsovariable, but may include an initial administration followed bysubsequent administrations. The dosage may also depend on the route ofadministration and will vary according to the size of the host.

The concentration of the immunogens in an immunogenic compositionaccording to the invention is in general about 1 to about 95%.Immunogenicity can be significantly improved if the antigens areco-administered with adjuvants, commonly used as 0.005 to 0.5 percentsolution in phosphate buffered saline. Adjuvants enhance theimmunogenicity of an antigen but are not necessarily immunogenicthemselves. Adjuvants may act by retaining the antigen locally near thesite of administration to produce a depot effect facilitating a slow,sustained release of antigen to cells of the immune system. Adjuvantscan also attract cells of the immune system to an antigen depot andstimulate such cells to elicit immune responses.

Immunostimulatory agents or adjuvants have been used for many years toimprove the host immune responses to, for example, vaccines. Thevaccines of the present invention may be used in conjunction with anadjuvants, for example, lipopolysaccharides, aluminum hydroxide andaluminum phosphate (alum), saponins complexed to membrane proteinantigens (immune stimulating complexes), pluronic polymers with mineraloil, killed mycobacteria in mineral oil, Freund's complete adjuvant,bacterial products, such as muramyl dipeptide (MDP) andlipopolysaccharide (LPS), as well as lipid A, and liposomes. Desirablecharacteristics of ideal adjuvants include: (1) lack of toxicity; (2)ability to stimulate a long-lasting immune response; (3) simplicity ofmanufacture and stability in long-term storage; (4) ability to elicitboth CMI and HIR to antigens administered by various routes; (5) synergywith other adjuvants; (6) capability of selectively interacting withpopulations of antigen presenting cells (APC); (7) ability tospecifically elicit appropriate T-cell helper 1 (TH 1) or TH 2cell-specific immune responses; and (8) ability to selectively increaseappropriate antibody isotype levels (for example, IgA) against antigens.An adjuvant used with the present invention need not possess all thesecharacteristics to be used with the present invention.

The route of administration for any one of the embodiments of thevaccine of the present invention includes, but is not limited to,oronasal, intramuscular, intraperitoneal, intradermal, subcutaneous,intravenous, intraarterial, intraocular, and oral as well as transdermalor by inhalation or suppository. The vaccine can be administered by anymeans which includes, but is not limited to, syringes, nebulizers,misters, needleless injection devices, or microprojectile bombardmentgene guns (Biolistic bombardment).

In one aspect of the invention, when the vaccine is subunit, DNA orrecombinant based, the present inventors contemplate that it may bepossible to use a single M protein and vary only the GP5 protein, forexample, its glycantype, and still obtain protection against PRRSV.

Alternatively, more than one glycan type of GP5, M, or GP5-M heterodimerof PRRSV may be employed in a vaccine according to the teachings of thepresent invention. This includes GP5, M, or GP5-M heterodimers fromdiffering PRRSV as well as multiple copies of the same or similar GP5,M, or GP5-M heterodimer according to glycantyping. The present inventorcontemplates that any vaccine for treating PRRS of the present inventionmay further include at least one other vaccine to a pig pathogen, forexample, swine influenza virus (SIV), porcine circovirus (PCV),Mycoplasma hyopneumoniae, or Haemophilus parasuis.

As one measure of vaccine potency, an ELISA can be performed on a samplecollected from an individual vaccinated to determine whether antibodiesto a vaccine comprising a PAD polypeptide, a derivative, a homologue ora variant or fragment thereof generated anti-PAD antibodies. Theindividual's sample is measured against a reference anti-PAD antibody.

The present vaccine's potency may also be measured by determiningwhether the vaccination protects a pig against infection by PRRSV. Avaccine protects a pig against infection by a PRRSV if, afteradministration of the vaccine to one or more unaffected pigs, asubsequent challenge with a biologically pure virus isolate (e.g., VR2385, VR 2386, or other virus isolate described below) results in alessened severity of any gross or histopathological changes (e.g.,lesions in the lung) and/or of symptoms of the disease, as compared tothose changes or symptoms typically caused by the isolate in similarpigs which are unprotected (i.e., relative to an appropriate control).More particularly, the present vaccine may be shown to be effective byadministering the vaccine to one or more suitable pigs in need thereof,then after an appropriate length of time (e.g., 1-4 weeks), challengingwith a large sample (10³⁻⁷ TCID₅₀) of a biologically pure PRRSV isolate.A blood sample is then drawn from the challenged pig after about oneweek, and an attempt to isolate the virus from the blood sample is thenperformed. Isolation of the virus is an indication that the vaccine maynot be effective, and failure to isolate the virus is an indication thatthe vaccine may be effective.

Thus, the effectiveness of the present vaccine may also be evaluatedquantitatively (i.e., a decrease in the percentage of consolidated lungtissue as compared to an appropriate control group) or qualitatively(e.g., isolation of PRRSV from blood, detection of PRRSV antigen in alung, tonsil or lymph node tissue sample by an immunoperoxidase assaymethod, etc.). The symptoms of the porcine reproductive and respiratorydisease may be evaluated quantitatively (e.g., temperature/fever),semi-quantitatively (e.g., severity of respiratory distress, orqualitatively (e.g., the presence or absence of one or more symptoms ora reduction in severity of one or more symptoms, such as cyanosis,pneumonia, heart and/or brain lesions, etc.).

Thus, the present invention also provides a method for vaccinating asusceptible host, for example, a pig, to PRRSV comprising administeringto the host a PAD polypeptide, a derivative, a homologue or a variant ora fragment thereof in an amount effective for protecting against PRRSVinfection. It will also be recognized by one of ordinary skill in theart that nucleic acids expressing a PAD polypeptide, a derivative, ahomologue or a variant or a fragment thereof may also be used invaccination. In another embodiment, a method for preventing or treatingPRRSV in an animal is provided wherein a therapeutically effectiveamount of a vaccine, PAD polypeptides or nucleic acids encoding PAD, asdescribed above, is administered to said animal. In one aspect, theanimal is a pig.

The present invention also contemplates that a novel PAD polypeptide, aderivative, a homologue or a variant or a fragment thereof or nucleicacids encoding PAD polypeptides of this invention, either alone or withother immunogenic polypeptides, may be administered to an animal, forexample, a pig, using any number of delivery systems or methods. Theseinclude but are not limited to a liposome delivery system, nakeddelivery system, electroporation, viruses, vectors, viral vectors, or aningestible delivery system wherein the PAD polypeptide or nucleic acidsencoding PAD are consumed, for example, in feed or water. Moreover, thePAD polypeptides, derivative, a homologue or a variant or fragmentthereof or nucleic acids encoding PAD polypeptides may be administered(or formulated for administration) peritoneally, orally, intranasally,subcutaneously, intradermally, intramuscularly, topically orintravenously, but may be administered or formulated for administrationby any pharmaceutically effective route (i.e., effective to produceimmunity). In another aspect, the method further comprises the PADpolypeptide, a derivative, a homologue or a variant or fragment thereofor nucleic acids encoding a PAD polypeptide being present in aphysiologically-acceptable carrier in an amount effective for protectingagainst PRRSV infection.

In addition to use as vaccines, the PAD polypeptides and nucleic acidsencoding PAD polypeptides disclosed herein are available for use asantigens to generate the production of antibodies for use in passiveimmunotherapy, for use as diagnostic reagents, and for use as reagentsin other processes such as affinity chromatography.

According to a still related aspect, the invention also includesso-called “passive immunization” methods for preventing or treatingPRRSV. For example, an antiserum comprising antibodies produced byimmunizing a heterologous host with PRRSV or mutant thereof, orimmunogenic fragment thereof, is used for the therapeutic treatment of aPRRSV-infected pig. However, even vaccines which provide activeimmunity, i.e., vaccines comprising PRRSV or mutants thereof, orimmunogenic fragments thereof, have been shown in certain cases to beeffective when given as a therapeutic treatment against variousdiseases. Thus, the immunity that is provided by the present inventioncan be either active immunity or passive immunity and the intended useof the vaccine and antiserum can be either prophylactic or therapeutic.

According to this aspect of the invention, animal subjects, e.g. pigs,are given an effective dosage of an antibody that specifically binds toa PAD polypeptide, a derivative, a homologue or a variant or fragmentthereof of the present invention. According to a related embodiment,such methods and compositions may include combinations of antibodiesthat bind at least one or more PAD polypeptides. The antibodies may alsobe administered with a carrier, as described herein. In general, inaccordance with this aspect of the invention, such antibodies, will beadministered (or formulated for administration) peritoneally, orally,intranasally, subcutaneously, intramuscularly, topically orintravenously, but can be administered or formulated for administrationby any pharmaceutically effective route (i.e., effective to produce theindicated therapeutic levels). Thus, among others, antibodies againstPRRSV may be employed to inhibit and/or treat PRRSV infections.

The invention further relates to diagnostic and pharmaceutical kitscomprising one or more containers filled with one or more of theingredients of the aforementioned compositions of the invention, forexample, nucleic acids encoding a PAD polypeptide, a PAD polypeptide, aderivative, a homologue or a variant or fragment thereof, or an antibodydirected towards a PAD polypeptide, a derivative, a homologue or avariant or a fragment thereof or a vaccine including a PAD polypeptideor a nucleic acid encoding a PAD polypeptide. Thus, the polynucleotides,polypeptides, and antibodies, and vaccines of the present invention maybe employed as research reagents and materials for treatments of anddiagnostics for PRRSV. In particular, it is contemplated that the kitsmay be used to determine whether a pig was successfully vaccinated sothat antibodies directed towards PAD are present in the collectedsample. For example, a biological sample from an animal, e.g. a pig,vaccinated with a PAD polypeptide described above is collected andincubated with a PAD polypeptide or other anti-PAD antibody preparationfor a time sufficient for antibody binding to take place. The antibodybinding to the PAD polypeptide or other anti-PAD antibody preparation isdetected using methods known to one of ordinary skill in the art, forexample Western Blot analysis and/or ELISA assays.

The anti-PAD antibodies of the invention have various utilities. Forexample, anti-PAD antibodies may be used in diagnostic assays for PRRSV,e.g., detecting its expression in specific cells, tissues, or serum.Various diagnostic assay techniques known in the art may be used, suchas competitive binding assays, direct or indirect sandwich assays andimmunoprecipitation assays conducted in either heterogeneous orhomogeneous phases (Zola, Monoclonal Antibodies: A Manual of Techniques,CRC Press, Inc. (1987) pp. 147-158). The antibodies used in thediagnostic assays can be labeled with a detectable moiety. Detection ofan antibody of the present invention can be facilitated by coupling(i.e., physically linking) the antibody to a detectable moiety. Examplesof detectable moieties include various enzymes, prosthetic groups,fluorescent materials, luminescent materials, bioluminescent materials,and radioactive materials. Examples of suitable enzymes includehorseradish peroxidase, alkaline phosphatase, .beta.-galactosidase, oracetylcholinesterase; examples of suitable prosthetic group complexesinclude streptavidin/biotin and avidin/biotin; examples of suitablefluorescent materials include umbelliferone, fluorescein, fluoresceinisothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansylchloride or phycoerythrin; an example of a luminescent material includesluminol; examples of bioluminescent materials include luciferase,luciferin, and aequorin, and examples of suitable radioactive materialinclude I¹²⁵, I¹³¹, S³⁵ or H³. The detectable moiety should be capableof producing, either directly or indirectly, a detectable signal. Anymethod known in the art for conjugating the antibody to the detectablemoiety may be employed, including those methods described by Hunter etal., Nature, 144:945 (1962); David et al., Biochemistry, 13:1014 (1974);Pain et al., J. Immunol. Meth., 40:219 (1981); and Nygren, J. Histochem.and Cytochem., 30:407 (1982). The present inventors contemplate thatsuch diagnostic kits would be of value in eradication programs for PRRSVat multiple levels, including but not limited to an individual (farm),regional, and/or national level.

Anti-PAD antibodies also are useful for the affinity purification of PADfrom recombinant cell culture or natural sources. In this process, theantibodies against PAD are immobilized on a suitable support, such aSephadex resin or filter paper, using methods well known in the art. Theimmobilized antibody then is contacted with a sample containing the PADto be purified, and thereafter the support is washed with a suitablesolvent that will remove substantially all the material in the sampleexcept the PAD, which is bound to the immobilized antibody. Finally, thesupport is washed with another suitable solvent that will release thePAD from the antibody.

While the invention has been described with reference to PADpolypeptides, it is to be understood that this covers a derivative, ahomologue or a variant or fragment thereof and similar proteins withadditions, deletions or substitutions which do not substantially affectthe protective antigenic properties of the recombinant protein.

The vaccine composition containing the attenuated PRRSV of the inventionare administered to a pig susceptible to or otherwise at risk of PRRSVinfection to enhance the pig's own immune response capabilities. Such anamount is defined to be an “immunogenically effective dose”. In thisuse, the precise amount again depends on the pig's state of health andweight, the mode of administration, the nature of the formulation, etc.Vaccine compositions may further incorporate additional substances tostabilize pH, or to function as adjuvants, wetting agents, oremulsifying agents, which can serve to improve the effectiveness of thevaccine. Vaccines are generally formulated for parenteral administrationand are injected either subcutaneously or intramuscularly. Such vaccinescan also be formulated as suppositories or for oral administration,using methods known in the art.

The amount of vaccine sufficient to confer immunity to PRRSV isdetermined by methods well known to those skilled in the art. Thisquantity will be determined based upon the characteristics of thevaccine recipient and the level of immunity required. Typically, theamount of vaccine or dosage to be administered will be determined basedupon the judgment of a skilled veterinarian or can be readily determinedby routine experimentation. The amount of virus vaccine of each strainmay be adjusted, i.e. increased or decreased, to result in a formulationwhich provides sufficient protection from infection with the desiredPRRSV. The present inventors contempate that different strains may becombined in any amount determined to be effective in preventing ortreating PRRSV infection of a strain in the vaccine formulation, andpossibly other strains if crossprotection occurs. Cross-protection toinfection by other PRRSV strains my depend on the order in which PRRSVstrains are administered or whether the pig has been subjected to aprior PRRSV infection as described above.

According to the present invention, the different PRRSV or PADs of PRRSVof the invention, for example, PADs of GP5, M, and/or GP5-M heterodimerwith the same or varying glycosylation patterns in the GP5 ectodomain,may be administered sequentially or progressively or alternatelyadministered simultaneously in an admixture. Sequential or progressiveadministration of the vaccine compositions of the invention may berequired to elicit sufficient levels of immunity to multiple PRRSVstrains. Single or multiple administration of the vaccine compositionsof the invention can be carried out. Multiple administration may berequired to elicit sufficient levels of immunity. Levels of inducedimmunity can be monitored by measuring amount of neutralizing secretoryand serum antibodies, and dosages adjusted or vaccinations repeated asnecessary to maintain desired levels of protection.

In one aspect of the immunization protocol against a PPRSV infection, avirus having a PAD of a GP5-M heterodimer of PRRSV of the presentinvention with glycosylation at position 44 of GP5 in a North Americanstrain is administered, followed by administration of a virus having aPAD of a GP5-M heterodimer of PRRSV of the present invention withoutglycosylation at position 44 of GP5 in a North American strain, and thenchallenged with a PRRSV having glycosylation in the neutralizing epitopeof GP5.

In another aspect, a virus having a PAD of a GP5-M heterodimer of PRRSVof the present invention with glycosylation at position 46 in GP5 in aEuropean strain is administered, followed by administration of a virushaving a PAD of a GP5-M heterodimer of PRRSV of the present inventionwithout glycosylation at position 46 in GP5 in a European strain, andthen challenged with a PRRSV having glycosylation in the neutralizingepitope of GP5.

In one aspect of the immunization protocol against a PPRSV infection, aPAD comprising a GP5-M heterodimer of PRRSV of the present inventionwith glycosylation at position 44 of GP5 in a North American strain isadministered, followed by administration of a PAD comprising a GP5-Mheterodimer of PRRSV of the present invention without glycosylation atposition 44 of GP5 in a North American strain, and then challenged witha strain of PRRSV having glycosylation in the neutralizing epitope ofGP5. In another aspect, a PAD comprising a GP5-M heterodimer of PRRSV ofthe present invention with glycosylation at position 46 of a GP5 in aEuropean strain is administered, followed by administration of a PADcomprising a GP5-M heterodimer of PRRSV of the present invention withoutglycosylation at position 46 of GP5 in a European strain, and thenchallenged with a strain of PRRSV having glycosylation in theneutralizing epitope of GP5.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-35 in the NA PRRSV GP5 protein. In another aspect, aPAD of GP5 may have a glycan at position 44 in the NA PRRSV GP5 protein.In another aspect, a PAD of GP5 may have a glycan at position 44 in theNA PRRSV GP5 and have glycans present or absent in amino acids 1-35 inthe NA PRRSV GP5 protein, for example, as found in some NA PRRSVstrains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-35 in the NA PRRSV GP5 protein. In anotheraspect, a PAD of GP5-M heterodimer may have a glycan at position 44 inthe NA PRRSV GP5 protein. In another aspect, a PAD of GP5-M heterodimermay have a glycan at position 44 in the NA PRRSV GP5 and have glycanspresent or absent in amino acids 1-35 in the NA PRRSV GP5 protein, forexample, as found in some NA PRRSV strains.

In one embodiment of the invention, a PAD of GP5 may have no glycansfrom amino acids 1-37 in the EU PRRSV GP5 protein, as found in Lelystad.In another aspect, a PAD of GP5 may have a glycan at position 46 in theEU PRRSV GP5 protein. In another aspect, a PAD of GP5 may have a glycanat position 46 in the EU PRRSV GP5 and have glycans present or absent inamino acids 1-37 in the EU PRRSV GP5 protein, for example, as found insome EU PRRSV strains.

In one embodiment of the invention, a PAD of GP5-M heterodimer may haveno glycans from amino acids 1-37 in the EU PRRSV GP5 protein, as foundin Lelystad. In another aspect, a PAD of GP5-M heterodimer may have aglycan at position 46 in the EU PRRSV GP5 protein. In another aspect, aPAD of GP5-M heterodimer may have a glycan at position 46 in the EUPRRSV GP5 and have glycans present or absent in amino acids 1-37 in theEU PRRSV GP5 protein, for example, as found in some EU PRRSV strains.

EXAMPLES Example 1

The solution to identification of the PAD of PRRSV was not obviousbecause others have not synthesized the information concerning NorthAmerican and European strains of PRRSV and Equine Arteritis Virus (EAV)into knowledge. For example, the modified live vaccine (MLV) for EAV isvery efficacious while the MLV for PRRSV is not. Thus many scientistsapparently have concluded that a comparison of the similarities anddifferences between the two viruses would not be of value regarding thedevelopment of a vaccine for PRRSV. Beginning in early February 2005,the inventors studied numerous publications, synthesized the variousimportant information, and by deductive reasoning identified theprotective antigenic determinants of PRRSV as the Matrix-Glycoprotein 5(M-GP5) heterodimer.

One of the most interesting and puzzling aspects of PRRS epidemiology isthe variation between North American and European isolates and the factthat at least before introduction of PRRSV live vaccine into Europe fromthe U.S., PRRS was relatively mild disease in western Europe. Inaddition, in some small traditional U.S. farms, the PRRSV spontaneouslydisappears for no apparent reason. Whereas in the U.S., PRRS has alwayscaused more devastating economic losses (especially in large herds). Forthis reason the inventors compared the N-Glycosylation sites on VR2332(the common N. American strain) and Lelystad virus (the common Europeanstrain) See Table 1. Please note the similarity of HLV013 and Lelystadvirus; however, these 2 viruses are not identical in that the GP5 signalsequence and hypervariable regions of GP5 are very different. Accordingto publications, there is evidence that live Lelystad virus may protectpigs against PRRS to a higher degree than VR 2332. The lack ofglycosylation at AA 1-43 is the reason that PRRS has been less severe inpart of Europe and in some farms in the U.S. That is, Lelystad virus hasbeen naturally immunizing pigs in Europe and strains similar to HLV013have been doing the same on a limited number of farms in the U.S. Thefact that N. American strains VR2332 and Mn184 are quite differentregarding glycosylation led us to compare antibody reactivity of VR2332and Leylstad strains (Table 2). Since antibody to the Lelystad virusreacts with the GP5-M heterodimer of Lelystad we hypothesized that theGP5-M heterodimer contains the protective antigenic determinants ofPRRSV and could be the basis for resistance to the PRRS.

TABLE 1 Comparison of AA sequence and N-glycosylation of various PRRSVstrains N-Glycosylation HLV Sites VR 2332* HLV092 HLV013 Lelystad HLV093094 1-43 or 45 + + − − + + 44 or 46 + + + + − + 51 or 53 + + + + + −*Ingelvac MLV, Ingelvac ATP and PrimePac MLV all similar to VR2332the inventors were aware that the MLV vaccine for EAV was quiteefficacious. Therefore the inventors compared the various immunologicaland genomic aspects of PRRSV to EAV (Table 3).

TABLE 2 Comparison of the antibody reactivity of VR2332 and Leystadstrains by Western Blot GP5-M Sera from infected Nucleocapsid Matrix GP5Heterodimer pigs with VR L VR L VR L VR L Ab to VR2332 + + + + − −  ?* ?(VR) Ab to Lelystad + + + +  −** + ? + (L) *? indicates that the resulthas not been published **Positive by peptide ELISA

TABLE 3 Comparison of PRRSV and EAV with regard to deducing theprotective antigenic determinants of PRRSV Characteristics PRRSV EAVHost Swine Equine Cultivatable in vitro Yes Yes GP5 main virusneutralizing (VN) epitope Yes Yes Antibody to GP5 induces immunity No NoWeak VN activity on nucleocapsid (N) and Yes Yes matrix (M) Antibody toN, M, and other GPs induces No No immunity Modified live vaccine (MLV)induces No Yes immunity to all strains of the virus MLV induces antibodyto N of all strains Yes  No* MLV induces antibody to M of all strainsYes Yes MLV induces antibody to GP5 of all strains No Yes MLV inducesantibody to M-GP5 heterodimer ?** Yes of all strains Antibody to GP5-Mheterodimer protects ?** Yes against disease M-GP5 heterodimer has beensynthesized No Yes Heparin receptor on M Yes ? Sialic acid on GP5 Yes ?N-glycosylation of asparagines on signal Yes No sequence andhypervariable regions which are to the left of the conserved VN epitopeof the AA sequence of the GP-5 protein N-glycosylation of asparagines onthe Yes Yes conserved VN epitope of the AA sequence of the GP-5 proteinA cysteine residue is in the AA sequence Yes Yes of the GP-5 protein Mand GP-5 are connected by a disulfide Yes Yes bond *The horse appearsnot to respond to the nucleocapsid of EAV; males which carry the virusin their testes may have antibodies to N. **Has not been published⁺Since EAV has no N-glycosylation sites to the left of the VN conservedepitope, the GP5-M heterodimer contains the protective antigenicdeterminants of PRRS by deductive reasoning.

Note that GP5 in PRRSV is synonymous with the envelope protein G_(L) inEAV. By synthesis and deduction, the identification of protectiveantigenic determinants (PAD) were identified. The PAD of PRRSV are theantigens associated with the GP5-M heterodimer and thus the basis ofthis disclosure. Plagemann, Faaberg, and Osorio have been focused simplyon the virus neutralizing (VN) aspects of PRRSV associated with GP5protein. But antibodies are not simply virus neutralizing, thus in PRRSVprotection, antibodies interfere with the heparin receptor on the matrixprotein and the sialic acid component of GP5 which prevent attachmentand entry into porcine alveolar macrophages (Table 3). The concept ofantibody inhibition in this disclosure is not virus neutralization perse. In summary,

-   -   Strains Lelystad and HLV013 of PRRSV have no glycans at residues        1-43 amino acids (AA) (in the signal sequence or the        hypervariable region upstream of the conserved neutralizing        epitope)    -   Antibodies to virulent and vaccine viruses of PRRSV do not react        with the GP5-M heterodimer of all PRRSV isolates because of the        presence of glycans at 1-43 AA    -   The glycans at 1-43 AA of the PRRSV on GP5 are the decoy epitope        A (Osorio) and the excess glycans (Plagemann) but these workers        believe the decoy glycans only interfere with the production of        virus neutralizing (VN) antibodies against the conserved region        in GP5 (they make no mention of the importance of matrix        protein).    -   In reality, the decoy glycans interfere with the production of        antibodies to the GP5-M heterodimer rather than just        interference with the production of VN antibodies to GP5.        Antibodies to GP5-M heterodimer prevent the attachment and entry        of PRRSV to porcine alveolar macrophages (not just virus        neutralization). Antibodies are only induced by live PRRSV if AA        1-43 are devoid of glycans thus the reason current MLV PRRSV        vaccines are ineffective.

PRRSV researchers have focused on the classical approaches to developingvaccines for viruses which involve mechanisms associated with eithercell mediated immunity (CMI) and/or virus neutralizing (VN) antibodies.Plagemann, Faaberg, and Osorio have identified a conserved epitope onGP5 which is associated with VN antibodies. However, antibodies to GP5conserved epitope alone do not induce sufficient protective antibodiesto PRRSV. Plagemann and Faaberg have suggested that the glycans on GP5may interfere with the production of VN antibodies and Osorio hassuggested that a decoy epitope prevents the production of VN antibodies.Osorio has injected sows with serum containing VN antibodies andprotected their piglets against PRRSV; however, when young piglets wereinjected with the antibody preparation, they were not protected. Youngpiglets were not protected because Osorio's antiserum lacked a completeset of antibodies to PAD (all the viruses used by Osorio to induce VNantibodies contained glycans in AA 1-43 of GP5). Thus, the antibodies toPAD are very different than the VN antibodies directed towards the GP5protein only.

Murtaugh has evidence that VN antibodies are not involved in eliminationof the virus in naturally affected pigs and favors a mechanism involvingCMI. Murtaugh stated at a recent meeting in Toronto (5 Mar. 2005) thatthe protective determinants of PRRSV have not been described.Publications by these experts and others in PRRSV research (attached)have repeatedly stated that PRRSV is unique virus that produces someresistance to homologous virus and very little protection toheterologous virus challenge and that CMI and VN responses are slow todevelop and are not necessarily associated with resistance to the virus.What has not been obvious to other scientists is that the PAD are acombination of the conserved region of the GP5 protein attached to thematrix in a heterodimer form. Furthermore, the GP5 protein must notcontain N-glycosylated asparagines between amino acids 1-43. It has beenpublished that the matrix protein (heparin receptors) is involved invirus attachment to porcine alveolar macrophages (PAM) of the pig andthat the GP5 protein contains sialic acid residues which allow entry toPAM. Thus, antibodies to PAD (GP5-M heterodimer) prevents PRRSVattachment and entry rather than just performing virus neutralization.Currently available vaccines do not produce antibodies to PAD of thePRRSV.

Example 2

Recent work in our lab showed that a live strain of PRRSV (FIG. 2,Strain HLV013) lacking the glycans prior to amino acid 44 of GP5 wouldinduce high titers to the GP neutralizing epitope as determined by aneutralizing peptide ELISA assay. Further analysis of HLV013 via Westernimmunoblotting indicated a stronger, earlier antibody response to GP5and GP5-M heterodimer when compared to VR2332 and sera from HLV013infected pigs showed more cross-reaction with PRRSV strain IA97-7895than did sera from VR2332 infected pigs (FIGS. 2 and 3). Results fromthese studies have led us to believe that N-glycosylation patterns inassociation with the GP5-M heterodimer are important components of amore effective neutralizing antibody response.

The influence of glycosylation on the evolution of neutralizingantibodies was first shown in this experiment. In this experiment, 3groups of 6 PRRSV negative pigs were treated as shown in Table A. Pigswere inoculated on Day 0 and again on Day 28 followed by inoculationwith a heterologous strain on Day 90. Serum was collected during thecourse of the study and assayed for neutralizing antibodies against theinoculating and heterologous strains (FIG. 4).

TABLE A Pig inoculation Trial 1 design Group # Day 0 (prime) Day 42(boost) 1 PBS PBS 2 VR2332 VR2332 3 HLV013 HLV013This trial provides evidence that there is a large difference betweenthe protective antibody responses to strains that differ inglycosylation. See FIG. 5. HLV013 lacking glycans prior to aa44 had afaster, more robust antibody response pre-challenge with morecross-reactivity when compared to VR2332. Post-challenge pigs inoculatedwith HLV013 had a faster anamnestic response and a faster response timein generating antibodies to the challenge strain.The below table corresponds to the Western blot in FIG. 5.

Primary antibody HLV013 MN184 VR2332 Lane # source Protein FFN FFN FFN 1NA Ladder NA NA NA 2 Group 1 Purified PRRSV 128 8 16 HLV013 3 Group 1Purified PRRSV 128 8 16 MN184 4 Group 1 Purified PRRSV 128 8 16 VR2332 5Group 2 Purified PRRSV 2048 256 256 HLV013 6 Group 2 Purified PRRSV 2048256 256 MN184 7 Group 2 Purified PRRSV 2048 256 256 VR2332Each lane contains 10 ug of purified PRRSV. Primary antibodies werediluted 1:100 and secondary antibody was diluted 1:2000.

Example 3 Animal Inoculation

Two 2-3 week old pigs were obtained from a source with no detectablepresence of PRRSV and housed at ISU research facilities. Followingacclimatization, pigs were infected intranasally with 10⁵ TC-ID₅₀ of thedesired strain. Pigs were bled on days −7, 0, 7, 21, 35, and 70post-inoculation to allow adequate time for production of neutralizingantibodies followed by humane euthanasia. Sera was aliquoted and sent toISU Diagnostic Lab for anti-N antibody ELISA (Herdcheck, IDEXX), SDSUDiagnostic Lab for MARC 145 serum neutralization assay (FFN), andUniversity of Minnesota for neutralizing peptide ELISA (Plagemann).Remaining sera was used for inhibition of AM infection testing at ISU.

This experiment was conducted in order to further evaluate the abilityof strains deficient in GP5 N-glycans to generate high titers ofneutralizing antibodies and their cross-reactivity. Pigs negative forPRRSV were obtained and randomized into 3 groups as shown in Table B. Atthe termination of the trial, serum was collected from all pigs andassayed for virus neutralizing antibodies against a variety of differentPRRSV strains (Table C).

TABLE B Group # Day 0 Day 70 Day 103 1 HLV013 HLV013 NA 2 HLV013 HLV093NA 3 HLV013 HLV093 NVSL 97-7895 All doses of PRRSV were 1 ml given IM ata dose of 1 × 10⁶ TCID₅₀/ml NA = not applicable

TABLE C Neutralizing antibody titers (geometric means) against variousstrains of PRRSV HLV NVSL SD VR MN Group 013 ISU-P 97-7895 PrimePac23983 2332 184 1 140.4 91.2 54.3 14.7 16.1 4.8 3.7 2 1216 512 363.1363.1 64.7 128.8 108.4 3 363.1 363.1 257 216.3 91.2 91.2 76.7Although all 3 groups generated homologous and heterologous neutralizingtiters, Group 2 had clearly higher titers. Addition of a thirdglycantype in Group 3 did not enhance the antibody response beyond whatwas demonstrated in Group 2. This indicates that the combination ofHLV013 and HLV093 are best suited for a universal vaccine to elicitheterologous neutralizing antibody.

The effect of the glycan shield can be further demonstrated by comparingthe geometric means of the geometric means against strain groups withthe same number of N-glycans prior to aa44. The 7 different strains usedin the FFN assay were divided into 3 different groups based onglycantype; NA-0, NA-1, and NA-2. We would expect to see the highesttiters against NA-0 strains and the lowest against NA-2 strainsregardless of GP5 sequence homology. This is indeed what we saw as shownin FIG. 6. This ability to predict cross-reaction of protectiveantibodies supports the use of glycantyping to define heterology amongstPRRSV strains.

Example 4 Collection of Alveolar Macrophages

AMs will be collected for culture as previously described (Mengeling,Thacker). Pigs (4-6 weeks old) will be anesthetized and euthanized byexsanguation. Lungs will be removed from the thoracic cavity forpulmonary lavage. Lavage fluid will consist of Dulbecco Modified EaglesMedium (DMEM) supplemented with gentamicin (0.5 mg/ml), penicillin (25U/ml), streptomycin (25 μg/ml), polymyxin B sulfate (3 U/ml), andamphotericin B (25 ug/ml). The lavage fluid will be dispensed andaspirated several times in order to collect the AMs. We expect tocollect 100-200 ml of lavage fluid per pig by pooling the aspiratedfluid from individual pigs. Fluid from different pigs will not be mixedto avoid immune reactions and to identify any differences in AMsusceptibility to PRRSV. Harvested fluid will be centrifuged at 1000 gfor 15 min, resuspended in 50 ml of PBS, and washed two more times. AMswill be counted and resuspended in PBS at a concentration ofapproximately 5×10⁷ AMs/1.5 ml followed by storage in liquid nitrogen.Batches will be validated by infecting AMs with PRRSV strain VR2332 andperforming immunoperoxidase monolayer assay (IPMA) with known positiveand negative sera to determine the TCID₅₀.

Example 5 Effect of Antibody Inhibition of Infection of AlveolarMacrophages

Polyclonal or monoclonal(s) antibodies will be diluted 2-fold and addedto 10⁵ TCID₅₀ of various homologous and heterologous PRRSV strains. Themixtures will be incubated for 1 hour at 37 C and then inoculated ontoalveolar macrophages (AMs) seeded in 96 well culture plates. Cells willbe incubated for 1 hour at 37 C with 5% CO2, washed, and incubated againuntil 10 hours post inoculation (Delputte). Cells will be fixed and thepercentage of infected cells will be calculated based onimmunoperoxidase staining. The t test will be used to compare percentageof infected cells between treatment and control wells.

Example 6 Immunoperoxidase Monolayer Assay

IPMA will be used to determine the percentage of infected cells asdescribed by Delputte et al. Briefly, fixed cells will incubated for 1hour at 37° C. with anti-nucleocapsid monoclonal antibody and 1/100diluted in PBS with 10% goat serum, followed by incubation for 1 hour at37° C. with peroxidase labeled goat anti-mouse Ig. Infected cells willbe visualized by a substrate solution of 3-amino-9-ethylcarbazole in0.05 M acetate buffer (pH 5) with 0.05% H₂O₂. Reaction will be blockedby washing with acetate buffer. Viral positive cells and total cellswill be counted by light microscope to determine percentage of infectedcells.

Example 7 Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis(SDS-PAGE)

Equal volume of antigen will be mixed with 2×LDS loading buffer(Invitrogen) either including reducing agent or without reducing agent.All samples will be boiled for 5 minutes. Using 4-12% pre-made gradientNovex Nu-PAGE gels (Invitrogen) and an XCell SureLock mini-cell(Invitrogen), 15 μl of each sample will be loaded into their respectivewells. SeeBlue Plus2 pre-stained ladder will be loaded in the first andlast wells at a volume of 10 μl. Once the gel is loaded and both thebuffer core and the lower buffer chamber are filled with 1×MES buffer(Invitrogen), the power supply current is set to 200 V and allowed torun for 45 minutes.

Example 8 Western Immunoblotting

Western blots will be used to further analyze and identify protectiveepitopes. Four blotting pads will be soaked in transfer buffer,consisting of 25 mM Bis-Tris, 25 mM Bicine, 1 mMEthylenediaminetetraacetic acid (EDTA) with 10% Methanol. ThePolyvinylidene fluoride (PVDF) will be briefly soaked in methanol andthen placed in transfer buffer. Two blotting filter paper sheets will besoaked in transfer buffer. All are placed at 4° C. with remainingtransfer buffer until the gel has finished. Once SDS-PAGE is completed,the gel cassette is removed and opened. After loading blottingmaterials, the blot module is filled with transfer buffer and the bufferchamber is filled with Nano purified water. The current will be set to170 mA and 30 V and allowed to run for 75 minutes. The membrane will beremoved from the blotting sandwich and transferred to a tray and coveredin blocking buffer, ELISA wash with Fish Gelatin (1.5 mM KH₂PO₄, 20 mMNa₂HPO₄, 134 mM NaCl, 2.7 mM KCl, 0.05% Tween-20 with 0.25% FishGelatin). The membrane will be left in the blocking buffer overnight at4° C. A 1:4000 dilution of swine serum will be made in 20 ml of blockingbuffer. Blocking buffer will be poured off and swine serum dilution isadded and allowed to rock at room temperature for 60 minutes. The swineserum dilution will be poured off and the membrane will be washed in 20ml of ELISA wash for 10 minutes, rocking at room temperature. Wash willbe poured off and the wash steps will be repeated twice for a total ofthree washes. During the last wash step, Biotin-SP conjugated Affinipuregoat anti-swine IgG (Jackson Immuno Research) will be diluted 1:2000 in20 ml of blocking buffer. After the final wash, goat anti-swine dilutionwill be poured onto the membrane and allowed to rock at room temperaturefor 60 minutes. Three wash steps will be repeated as previouslydescribed. A 1:2000 dilution of streptavidin Hrp (Zymed) in 20 ml ofblocking buffer is prepared and poured onto the PVDF membrane, rockingat room temperature for 60 minutes. Three wash steps are repeated again.During the final wash step, TMB Membrane Peroxidase Substrate System(KPL) will be prepared by mixing in a small tray 12.5 ml of TMBPeroxidase Substrate, 12.5 ml Peroxidase Solution B and 2.5 ml TMBMembrane Enhancer. Once washing is complete, wash is poured off and themembrane is submerged in the substrate for 1 minute or until desiredcolor of horseradish peroxidase is achieved without intense background.PVDF membrane will be dried and covered in clear plastic and scanned forelectronic record of western blot.

Example 9 Quantitative Real-Time PCR

Quantitative real-time PCR (qRT-PCR) will be used as another method tocompare the ability of antibodies to prevent binding and infection ofAMs. Following infection and incubation of AM with antibody and PRRSV asdescribed above, cells will be washed three times to removeextracellular, unbound virus and antibody-virus complexes. AMs will beharvested, lysed, and viral RNA extracted using the Qiagen Virus SpinKit. Extract will then be assayed by qRT-PCR (Tetracore) on the Bio-RadiCycler iQ and compared to a standard curve. The cycling conditions willbe as follows: 1) RT step: 52° C. for 1800 seconds 2) Enzyme activationstep: 95° C. for 900 seconds, 3) 3-step PCR: 40 cycles (changed fromTetracore's recommended 50 cycles) of (94° C. for 30 seconds, 61° C. for60 seconds, and 72° C. for 60 seconds).

Example 10 Production of Antibodies Against PRRSV in Pigs

Twenty 5 to 6 week old conventional PRRSV-free pigs will be injectedwith a vaccine against PAD of PRRSV. Serum from each pig will beevaluated bi-weekly for antibody to PRRSV detectable by ELISA, andinfection inhibition of alveolar macrophages (Erdman). Pigs will beinjected repeatedly on bi-weekly occasions if adequate antibody levelsare not attained. It is anticipated that pigs will be killed and bloodcollected for pooled serum 6 to 12 weeks post exposure. Twenty pigs ofthe same age will serve as uninfected controls and be the source ofnormal swine serum.

Example 11 Production of Antibodies Against PRRSV in Horses

Two horses will receive PAD polypeptide mixed in Freund's incompleteadjuvant by intramuscular injection followed by CVA only at bi-weeklyintervals for 8 weeks. Serum from horses will be evaluated by infectioninhibition of alveolar macrophages and Western blot analysis. Normalhorse serum will be collected by repeated samplings prior to theimmunization with CVA.

Example 12 Concentration of Antibodies to PAD of PRRSV

Plasma containing antibodies to PRRSV will be concentrated by removal oflipids and albumin by precipitation and subsequent ultrafiltration to90% globulin content.

Example 13 Challenge Model for Evaluation of Antibodies for ProtectionAgainst PRRSV

Hysterectomy-derived, colostrums-deprived (HDCD) pigs will be procuredfrom the Rexanne Struve Laboratory at 4-6 hours of age. Pigs will be feda diet of Esbilac milk replacer. The milk replacer of pigs in principalgroups will be supplemented with either pig or horse globulin containingantibodies to PAD of PRRSV. Control pigs will receive normal porcine orhorse globulin of the same concentration as pigs in the principalgroups. Esbilac containing globulin will not be fed after 36 hours ofage. All pigs will be challenged intranasally with PRRSV strain HLV092at 3 days of age. Each test preparation or combination will be evaluatedin 10 HDCD pigs which are simultaneously challenged with 10 controlpigs. One-half the pigs will be killed and necropsied 14 days afterchallenge and tissues (blood, lung, lymph nodes, tonsil) collected andassayed for presence of PRRSV by qPCR and virus isolation. Sentinel pigswill be placed with the remaining ½ pigs in each group to determine ifchallenged pigs are capable of transmission of the virus over the next 2week time period.

Example 14 Field Experiment on PRRSV Positive Farm

A PRRSV positive farm will be selected with the following approximatemortality rates—farrowing 15-20% and nursery 10-15%. Pigs within eachlitter will be randomly assigned to 2 groups. Concentrated normalglobulin (NG—Group 1) and PRRSV Ab concentrate generated against PAD(Group 2) will be orally administered prior to 24 hours of age andsubsequently by intraperitoneal injection based on half-lifedeterminations in the ISU experiments. The total number of pigs pergroup will be based on the number of pigs required to test a decrease inmortality rate by 10% in both farrowing and nursery. Statisticalsoftware (JMP 5.1.2, SAS Institute, Inc., Cary, N.C.) was used todetermine the sample size for comparing proportions of two independentgroups. At a power of 90%, 672 animals (336 per group) would be requiredto detect a 10% difference in mortality (from 20% to 10%) at the p<0.05level of significance. To detect a 10% difference in mortality (from 15%to 5%) at the same power and p level, 536 animals (268 per group) arerequired. Cause of death will be determined by complete necropsy andsubmission of samples for qPCR.

Example 15 Statistical Analysis

The quantitative data collected (virus titration, qPCR, antibody titers)will be analyzed using ANOVA. Chi square test for proportions will beused for categorical data (mortality rate, % lung involvement, presenceor absence of PRRSV). Analysis will be conducted using SAS statisticalsoftware and significance set at p≦0.05.

Example 16 Supportive Data from Laboratory and Pig Studies

TABLE 4 FFN data. Virus neutralization was tested on Marc 145 cells.Values indicate the reciprocal of the highest serum dilution exhibitingneutralization activity. Pigs (n = 6 per group) were inoculated on Day 0with a sham control, HLV013, or VR2332 PRRSV strains. On Day 14, HLV013group pigs were boostered (booster vaccinate shot) with HLV093. By day42 dpi, only the HLV013 group showed VN activity. All groups werechallenged with HLV092 on Day 90. The VN activity of the HLV013 groupcontinued to increase when tested against homologous and heterologousvirus. FFN-Values < 4 = Negative Result 42 dpi* 42 dpi 90 dpi/0 dpc**104 dpi/14 dpc FFN VR VR 42 dpi SD VR HLV HLV SD VR HLV HL Group virus2332 2332 HLV013 23983 2332 092 013 23983 2332 092 V013 Control 2544 2  ND*** ND 2 2 2 2 2 2 2 2 2545 2 ND ND 2 2 2 2 2 2 2 2 2547 2 ND ND 2 22 2 2 2 4 2 2548 2 ND ND 2 2 2 2 2 2 2 2 2550 2 ND ND 2 2 2 2 4 4 2 2HLV013 2582 2 2 16 4 4 4 128 4 2 2 128 2583 2 2 8 4 2 4 128 4 4 2 162584 2 2 8 2 2 4 32 8 8 8 256 2585 2 2 4 2 2 2 64 8 8 64 >256 2586 2 2 48 8 8 256 8 8 16 128 2587 4 2 32 2 2 2 32 32 64 128 >256 VR2332 2594 2 42 4 8 2 4 32 32 8 16 2595 4 2 2 4 8 2 8 8 8 4 4 2596 4 2 2 8 16 8 8 4 82 2 2597 2 2 2 4 8 2 4 8 8 2 2 2598 4 4 2 8 16 2 4 64 32 32 4 2599 4 2 22 8 2 4 4 8 2 2 *Days post inoculation **Days post challenge ***NotDetermined

We have injected pigs with inactivated crude viral antigen comprisingGP5, M, and GP5-M heterodimer prepared from HLV013 and compared theELISA response (FIG. 15) to that of pigs injected with a commercialinactivated PRRS vaccine (Intervet). HLV013 induced rapid and highantibody titers as compared to the commercial vaccine.

A challenge study was conducted in which live HLV013 and VR2332 wereinoculated in experimental pigs and later challenged with a heterologousstrain (HLV092) of PRRSV (Table 6). Results indicated protection wasinduced by both viruses; however, resistance appeared to be induced morerapidly by HLV013. In experiment 1, strain HLV 093 was detected in theHLV013 group at 28 days post inoculation with HLV013. One method ofimmunization with live PRRSV is as follows:

Step 1—inject pigs with live HLV013 (FIG. 10) on Day 1Step 2—inject pigs with live HLV093 (FIG. 11) on Day 21Step 3—inject pigs with live HLV092 (FIG. 12) on Day 42Pigs immunized in these progressive steps will produce antibody to allthe protective components of PAD and thus heterologous protectionagainst most if not all of the current preponderant isolates of PRRSV inNorth America. Injection of animals with HLV092 first will not result inheterologous protection. For protection against European isolates, asimilar scheme may be needed but using isolates of the Europeanglycantypes, e.g. priming or administering with an European PRRSV strainthat has little or no glycosylation among amino acids 31-39 in the GP5ectodomain. For example, injection of pigs with LV does not induceantibodies to the GP 5 protein of VR2332 but it does induce antibodiesto GP5 and the GP5-M heterodimer of LV.

TABLE 7 Glycantyping Scheme developed by the inventors. According to thepresent invention, PRRSV strains within the North American and Europeangenotypes are grouped based on their glycosylation patterns. Thisdiscovery is referred to by the inventors as a glycantyping scheme.Glycantyping is a more accurate means of discerning heterologous PRRSVstrains as new strains emerge in the population than sequence homologyof ORF5. The present inventors contemplate that the discernment ofglycosylation patterns can be used in single or multivalent vaccines orin the development of vaccination schemes and protocols. Number ofpredicted PRRSV Glycantype^(a) glycans^(b,c) NA-0  0^(d) NA-1 1 NA-2 2NA-3 3 NA-4 4 NA-n n EU-0 0 EU-1 1 EU-2 2 EU-3 3 EU-4 4 EU-n n ^(a)NA =North American, EU = European. ^(b)Number of glycans located on theectodomain of GP5 excluding highly conserved glycans located at aa44 and51 for NA strains and aa46 and 53 for EU strains. When these glycans areabsent they should be noted as follows: if an NA-1 strain lacks a glycanat aa44 it is described as NA-1 (Δ44). ^(c)As the number of predictedglycans increases so does the resistance to inducing protective(neutralizing) antibodies and/or susceptibility to such antibodies.^(d)NA-0 and EU-0 are predicted to be the parent strains for all NA andEU strains respectively. Thus these viruses should be included inattempts to generate cross-reacting antibodies. After NA-0 and EU-0,glycantyping may be a predictor of heterology which is currently poorlydefined for PRRSV. *This scheme may be applicable to other RNA viruses.

TABLE 7a FFN data from pigs inoculated with HLV013 (two logs higher thanin Table 5). Blood was collected 42 days after inoculation. Virusneutralization was tested on Marc 145 cells. Values indicate thereciprocal of the highest serum dilution exhibiting neutralizationactivity. Virus used in neutralization assay Pig ID# HLV013 SD 23983VR2332 1 64 16 8 2 32 4 4 3 16 32 4 4 64 64 8 5 64 8 8 6 256 8 8 7 64 84 8 16 4 <4 9 128 16 8 10 64 8 4 11 16 <4 <4 12 32 <4 <4 13 64 32 8 1464 8 <4 15 64 8 <4 16 64 4 4 17 256 4 <4 18 128 4 4 19 64 32 4 20 >25616 16

TABLE 8 Data from virulent PRRSV (HLV092) challenge of pigs described inFIG. 16 and Tables 6-7. Severity Treatment of IP^(a) Pathology^(b)qPCR^(c) Controls - 4/5 PLH: 2 mild, 5 × 10⁷ Non-vacc 1 moderate Vacc -HLV013 0/5 PLH: 3 mild 0.00 Vacc - VR2332 0/5 PLH: 2 mild, 0.00 3 severe^(a)Number of pigs with an interstitial pneumonia (IP) lung score >2 ona scale of 1 to 6. ^(b)Number of pigs with either mild, moderate, orsevere peribronchiolar lymphoid hyperplasia (PLH) based onhistopathology. ^(c)Quantitative PCR (average viral copies per ml) fromserum 10 days post challenge.

TABLE 9PRRSV ORF 5 Sequencing. Nucleotide sequences were translated into aminoacid sequences¹ and N-glycosylation sites were predicted². Only the first 80 aa are shown,however genotypic relatedness (percent homology) is based on entire sequence (200 aa).Potential N-glycosylation sites are underlined.Please amend Table 9 at page 73 as follows: First 80 Amino Acids(N-glycosylation sites  SEQ ID Inoculating Virus in red highlighting)Glycans NO: HLV094 MLGRCLTAGC CSRLLSLWCI VPFCFAALVN  33, 44, 51 95ANSNSSSHLQ LIYNLTLCEL NGTDWLKDKF  DWAVETFVIF PVLTHIVSYG HLV013MLGRCLTAGC CSRLLSLWCI VPFCFVALVN  44, 51 96ANSNSGSHLQ LIYNLTLCEL NGTDWLKDKF  DWAVETFVIF PVLTHIVSYS HLV093MLGKCLTAGY CSQLPFLWCI VPFCLAALVN  33, 51 97ANNDSSSHLQ LIYSLTICEL NGTEWLNEHF  SWAVETFVIF PALTHIVSYG VR2332MLEKCLTAGC CSRLLSLWCI VPFCFAVLAN  30, 33, 44, 51 98ASNDSSSHLQ LIYNLTLCEL NGTDWLANKF  DWAVESFVIF PVLTHIVSYGFirst 80 Amino Acids Genotypic Pig Serum (N-glycosylation sites in Relatedness Group ID # Seq. # DPI red highlighting) Glycans to HLV013HLV013 2582  5436 HLV079 14 MLGRCLTAGC CSRLLSLWCI VPFCFVALVN 44, 51  100% 99 ANSNSGSHLQ LIYNLTLCEL NGTDWLKDKF DWAVETFVIF PVLTHIVSYS HLV0132582  5465 HLV083 28 MLGRCLTAGC CSRLLSLWCI VPFCFVALVN 34, 44, 99.67% 100ANSNSSSHLQ LIYNLTLCEL NGTDWLKDKF 51 DWAVETFVIF PVLTHIVSYS HLV013 2586*5440 HLV080 14 MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 44, 85.57% 101ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG HLV013 2586 5469 28 No PCR Product - two runs for  sequencing HLV013 2587  5441HLV081 14 MLGRCLTAGC CSRLLSLWCI VPFCFVALVN 44, 51   100% 102ANSNSGSHLQ LIYNLTLCEL NGTDWLKDKF DWAVETFVIF PVLTHIVSYS HLV013 2587  5470HLV086 28 MLGRCLTAGC CSRLLSLWCI VPFCFVALVN 44, 51 98.83% 103ANSNNGSHLQ LIYNLTLCEL NGTDWLKDKF DWAVETFVIF PVLTHIVSYS HLV094 2581* 5464HLV082 28 MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 44, 104ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG HLV093 2588*5471 HLV087 28 MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 41, 105ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG GenotypicRelatedness to HLV093 HLV013 2586  5440 HLV080 14MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 44, 99.84% 105ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG HLV094 2581 5464 HLV082 28 MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 44, 99.84% 105ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG HLV093 2588 5471 HLV087 28 MLGKCLTAGY CSQLPFLWCI VPFCLAALVN 33, 44, 99.84% 105ANNDSSSHLQ LIYNLTICEL NGTEWLNEHF  51 SWAVETFVIF PALTHIVSYG *Identicalgenotypes ¹ExPASy-Translate Tool ²NetNGlyc 1.0 Server″

DEPOSITS

A deposit of the viruses of HLV013, HLV092, HLV093, and MN184 is and hasbeen maintained by Dr. Delbert Harris, Room 45, Kildee Hall, Iowa StateUniversity, Ames, Iowa 50011, since prior to the filing date of thisapplication. Access to this deposit will be available during thependency of the application to the Commissioner of Patents andTrademarks and person determined by the Commissioner to be entitledthereto upon request. Upon allowance of any claims in the application,the Applicant(s) will make available to the public without restriction adeposit of at least 25 frozen or freeze-dried samples (1 ml each) ofHLV013, HLV092, HLV093, HLV094, and MN184 viruses with the American TypeCulture Collection (ATCC), Manassas, Va. 20110. The 25 frozen orfreeze-dried samples (1 ml each) of PRRSV of HLV013, HLV092, HLV093,HLV094, and MN184 viruses deposited with the ATCC will be taken from thesame deposit maintained at Room 45, Kildee Hall, Iowa State Universityand described above. Additionally, Applicant(s) will meet all therequirements of 37 C.F.R. §1.801-1.809, including providing anindication of the viability of the sample when the deposit is made. Thisdeposit of 25 frozen or freeze-dried samples (1 ml each) of HLV013,HLV092, HLV093, HLV094, and MN184 viruses will be maintained withoutrestriction in the ATCC Depository, which is a public depository, for aperiod of 30 years, or 5 years after the most recent request, or for theenforceable life of the patent, whichever is longer, and will bereplaced if it ever becomes nonviable during that period.

What is claimed is:
 1. A method of preparing a vaccine for generating aprotective response to exposure to PRRSV, the method comprising:determining the number of glycans of the glycoprotein 5 (GP5) of a PRRSVstrain, and preparing a vaccine comprising a GP5 having fewer glycansthan said PRRSV strain.
 2. A method of preparing a vaccine forgenerating a protective response to exposure to PRRSV, the methodcomprising preparing a vaccine comprising: a glycoprotein 5 (GP5) ofPRRSV, wherein said GP5 glycosylation is selected from the groupconsisting of no glycans, glycans present at position 44 in NorthAmerican PRRSV strains, glycans present at position 51 North AmericanPRRSV strains, glycans present at positions 44 and 51 North AmericanPRRSV strains, glycans present at position 46 in European PRRSV strains,glycans present at position 53 in European PRRSV strains, and glycanspresent at positions 46 and 53 of said GP5 protein in European PRRSVstrains.
 3. A method of grouping PRRSV strains, the method comprising:determining the number of glycans and the position of said glycans on aglycoprotein 5 (GP5) of PRRSV, and grouping said strain with strainshaving the same number of glycans at the same position.